Starting phenix.real_space_refine on Fri Feb 14 04:05:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mn5_23916/02_2025/7mn5_23916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mn5_23916/02_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_23916/02_2025/7mn5_23916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mn5_23916/02_2025/7mn5_23916.map" model { file = "/net/cci-nas-00/data/ceres_data/7mn5_23916/02_2025/7mn5_23916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mn5_23916/02_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-5592/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: 6.09, per 1000 atoms: 0.64 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 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: 1.27 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: 3.20 Time building geometry restraints manager: 2.98 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: 1.910 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.630 Find NCS groups from input model: 0.180 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- 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 0.084 9743 Z= 0.817 Angle : 1.465 8.723 13221 Z= 1.007 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 *********************** 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 : 1.190 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: 1.4263 time to fit residues: 221.7749 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 : 1.068 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 302 ASN B 318 HIS B 470 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.127388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087231 restraints weight = 16564.700| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.23 r_work: 0.3282 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9743 Z= 0.308 Angle : 0.685 14.947 13221 Z= 0.361 Chirality : 0.049 0.155 1473 Planarity : 0.005 0.039 1740 Dihedral : 7.694 64.895 1571 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.29 % Allowed : 6.76 % Favored : 90.95 % 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: -0.36 (0.24), residues: 1195 helix: -2.48 (0.46), residues: 95 sheet: -0.81 (0.42), residues: 138 loop : 0.16 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 205 HIS 0.012 0.001 HIS B 564 PHE 0.016 0.002 PHE A 94 TYR 0.014 0.002 TYR B 274 ARG 0.005 0.001 ARG B 354 *********************** 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 79 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.7977 (t0) cc_final: 0.7736 (t0) REVERT: A 158 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7814 (mmp) REVERT: H 181 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8157 (tmtt) REVERT: B 538 GLN cc_start: 0.7812 (pt0) cc_final: 0.7005 (pp30) outliers start: 24 outliers final: 7 residues processed: 72 average time/residue: 1.2678 time to fit residues: 98.9460 Evaluate side-chains 51 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 531 CYS 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: 0.6980 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 92 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.127822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087745 restraints weight = 16759.107| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.23 r_work: 0.3293 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9743 Z= 0.164 Angle : 0.556 15.171 13221 Z= 0.285 Chirality : 0.045 0.185 1473 Planarity : 0.005 0.040 1740 Dihedral : 6.615 58.696 1571 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.90 % Allowed : 7.33 % 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: -0.34 (0.24), residues: 1195 helix: -2.01 (0.52), residues: 88 sheet: -0.71 (0.44), residues: 136 loop : 0.08 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 510 HIS 0.005 0.001 HIS B 249 PHE 0.015 0.001 PHE A 543 TYR 0.007 0.001 TYR A 123 ARG 0.005 0.000 ARG B 354 *********************** 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 66 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8020 (t0) cc_final: 0.7621 (t0) REVERT: A 490 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7868 (tpp-160) REVERT: H 181 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8216 (tmtt) REVERT: B 238 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: B 277 ASP cc_start: 0.7644 (m-30) cc_final: 0.7436 (m-30) REVERT: B 538 GLN cc_start: 0.7792 (pt0) cc_final: 0.6974 (pp30) outliers start: 20 outliers final: 8 residues processed: 59 average time/residue: 1.4225 time to fit residues: 91.0253 Evaluate side-chains 52 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 193 HIS Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 116 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 25 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 400 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3944 r_free = 0.3944 target = 0.120563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079849 restraints weight = 16782.412| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.20 r_work: 0.3150 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 9743 Z= 0.490 Angle : 0.713 20.325 13221 Z= 0.358 Chirality : 0.052 0.150 1473 Planarity : 0.006 0.041 1740 Dihedral : 6.379 59.291 1571 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.67 % Allowed : 7.33 % 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: -0.63 (0.24), residues: 1195 helix: -1.98 (0.54), residues: 76 sheet: -0.91 (0.43), residues: 143 loop : -0.18 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 521 HIS 0.008 0.002 HIS B 174 PHE 0.023 0.003 PHE A 94 TYR 0.022 0.002 TYR B 274 ARG 0.005 0.001 ARG B 203 *********************** 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 73 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 45 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8225 (t0) cc_final: 0.7759 (t0) REVERT: A 475 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6381 (mmt-90) REVERT: A 490 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7781 (tpp-160) REVERT: H 181 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8264 (tmtt) REVERT: B 393 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7856 (mm110) REVERT: B 538 GLN cc_start: 0.7872 (pt0) cc_final: 0.7064 (pp30) outliers start: 28 outliers final: 14 residues processed: 69 average time/residue: 1.2174 time to fit residues: 91.2810 Evaluate side-chains 56 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 214 CYS Chi-restraints excluded: chain A residue 226 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 475 ARG 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 206 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 199 CYS 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: 2.9990 chunk 23 optimal weight: 0.0570 chunk 27 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 400 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 = 0.3982 r_free = 0.3982 target = 0.123269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082952 restraints weight = 16614.799| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.17 r_work: 0.3206 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9743 Z= 0.194 Angle : 0.556 17.483 13221 Z= 0.282 Chirality : 0.046 0.169 1473 Planarity : 0.004 0.036 1740 Dihedral : 5.675 54.772 1571 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.90 % Allowed : 8.95 % Favored : 89.14 % 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: -0.64 (0.24), residues: 1195 helix: -2.02 (0.53), residues: 82 sheet: -0.82 (0.44), residues: 143 loop : -0.18 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.009 0.000 ARG B 330 *********************** 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 62 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8148 (t0) cc_final: 0.7644 (t0) REVERT: A 490 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7773 (tpp-160) REVERT: H 181 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8241 (tmtt) REVERT: B 538 GLN cc_start: 0.7823 (pt0) cc_final: 0.7007 (pp30) outliers start: 20 outliers final: 10 residues processed: 59 average time/residue: 1.0246 time to fit residues: 66.6309 Evaluate side-chains 51 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 26 CYS Chi-restraints excluded: chain B residue 193 HIS 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: 0.8980 chunk 89 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 7 optimal weight: 0.0470 chunk 90 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3996 r_free = 0.3996 target = 0.124276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083957 restraints weight = 16671.041| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.20 r_work: 0.3212 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9743 Z= 0.159 Angle : 0.518 15.439 13221 Z= 0.262 Chirality : 0.045 0.181 1473 Planarity : 0.004 0.039 1740 Dihedral : 5.223 54.363 1571 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.19 % Allowed : 8.67 % Favored : 89.14 % 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 (0.25), residues: 1195 helix: -1.50 (0.58), residues: 75 sheet: -0.83 (0.46), residues: 136 loop : -0.07 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 205 HIS 0.002 0.000 HIS B 260 PHE 0.009 0.001 PHE A 219 TYR 0.007 0.001 TYR B 274 ARG 0.005 0.000 ARG B 354 *********************** 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 68 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8186 (t0) cc_final: 0.7727 (t0) REVERT: A 490 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7795 (tpp-160) REVERT: H 181 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8271 (tmtt) REVERT: H 186 GLU cc_start: 0.7407 (pm20) cc_final: 0.7052 (pm20) REVERT: B 538 GLN cc_start: 0.7798 (pt0) cc_final: 0.7008 (pp30) outliers start: 23 outliers final: 10 residues processed: 62 average time/residue: 1.1518 time to fit residues: 77.8857 Evaluate side-chains 53 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 490 ARG 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 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 564 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 41 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.123577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.083257 restraints weight = 16759.762| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.19 r_work: 0.3214 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9743 Z= 0.192 Angle : 0.529 16.213 13221 Z= 0.267 Chirality : 0.045 0.174 1473 Planarity : 0.004 0.038 1740 Dihedral : 5.199 55.213 1571 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.00 % Allowed : 9.14 % 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: -0.40 (0.25), residues: 1195 helix: -1.35 (0.60), residues: 74 sheet: -0.77 (0.47), residues: 133 loop : -0.06 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 205 HIS 0.003 0.001 HIS B 174 PHE 0.010 0.001 PHE A 94 TYR 0.016 0.001 TYR A 523 ARG 0.006 0.000 ARG B 354 *********************** 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 65 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8148 (t0) cc_final: 0.7695 (t0) REVERT: A 490 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7774 (tpp-160) REVERT: H 181 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8382 (tmtt) REVERT: H 186 GLU cc_start: 0.7379 (pm20) cc_final: 0.7031 (pm20) REVERT: B 538 GLN cc_start: 0.7806 (pt0) cc_final: 0.7008 (pp30) outliers start: 21 outliers final: 12 residues processed: 61 average time/residue: 1.1508 time to fit residues: 76.8418 Evaluate side-chains 56 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 236 SER 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 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 26 CYS Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 564 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.120128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079695 restraints weight = 16967.732| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.20 r_work: 0.3147 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9743 Z= 0.413 Angle : 0.647 19.677 13221 Z= 0.324 Chirality : 0.049 0.152 1473 Planarity : 0.005 0.037 1740 Dihedral : 5.694 58.138 1571 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.19 % Allowed : 9.33 % Favored : 88.48 % 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: -0.64 (0.24), residues: 1195 helix: -1.61 (0.58), residues: 75 sheet: -0.91 (0.45), residues: 143 loop : -0.23 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 452 HIS 0.007 0.001 HIS B 174 PHE 0.017 0.002 PHE A 94 TYR 0.018 0.002 TYR B 274 ARG 0.006 0.001 ARG B 354 *********************** 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 65 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8202 (t0) cc_final: 0.7703 (t0) REVERT: A 475 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6477 (mmt-90) REVERT: A 490 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7716 (tpp-160) REVERT: H 186 GLU cc_start: 0.7694 (pm20) cc_final: 0.7051 (pm20) REVERT: H 187 LYS cc_start: 0.8742 (tptm) cc_final: 0.8535 (tptm) REVERT: B 538 GLN cc_start: 0.7912 (pt0) cc_final: 0.7073 (pp30) outliers start: 23 outliers final: 15 residues processed: 59 average time/residue: 1.2058 time to fit residues: 77.3881 Evaluate side-chains 57 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 236 SER 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 111 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.120528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.080260 restraints weight = 16791.013| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.20 r_work: 0.3156 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9743 Z= 0.334 Angle : 0.602 18.351 13221 Z= 0.303 Chirality : 0.048 0.157 1473 Planarity : 0.005 0.035 1740 Dihedral : 5.590 56.300 1571 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.81 % Allowed : 9.90 % 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: -0.62 (0.25), residues: 1195 helix: -1.21 (0.61), residues: 68 sheet: -0.95 (0.44), residues: 153 loop : -0.24 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 205 HIS 0.005 0.001 HIS B 174 PHE 0.015 0.002 PHE A 94 TYR 0.015 0.001 TYR A 523 ARG 0.005 0.000 ARG B 354 *********************** 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: 19 poor density : 42 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8168 (t0) cc_final: 0.7659 (t0) REVERT: A 490 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7711 (tpp-160) REVERT: H 186 GLU cc_start: 0.7694 (pm20) cc_final: 0.7162 (pm20) REVERT: B 538 GLN cc_start: 0.7865 (pt0) cc_final: 0.7055 (pp30) outliers start: 19 outliers final: 12 residues processed: 57 average time/residue: 1.0863 time to fit residues: 68.0247 Evaluate side-chains 55 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 293 ASN 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 206 SER Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS 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 70 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3973 r_free = 0.3973 target = 0.122670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082591 restraints weight = 16921.805| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.20 r_work: 0.3187 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9743 Z= 0.163 Angle : 0.545 16.172 13221 Z= 0.272 Chirality : 0.045 0.176 1473 Planarity : 0.004 0.037 1740 Dihedral : 5.173 53.869 1571 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.43 % Allowed : 10.57 % Favored : 88.00 % 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: -0.52 (0.25), residues: 1195 helix: -1.40 (0.59), residues: 74 sheet: -0.71 (0.46), residues: 148 loop : -0.17 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 205 HIS 0.003 0.001 HIS B 249 PHE 0.013 0.001 PHE A 543 TYR 0.016 0.001 TYR A 523 ARG 0.005 0.000 ARG B 354 ********************** 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: 15 poor density : 46 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8115 (t0) cc_final: 0.7618 (t0) REVERT: A 490 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7700 (tpp-160) REVERT: H 186 GLU cc_start: 0.7708 (pm20) cc_final: 0.7184 (pm20) REVERT: B 538 GLN cc_start: 0.7815 (pt0) cc_final: 0.7041 (pp30) outliers start: 15 outliers final: 10 residues processed: 58 average time/residue: 1.0117 time to fit residues: 64.8445 Evaluate side-chains 54 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 193 HIS 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: 1.9990 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 0.0370 chunk 69 optimal weight: 0.0060 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 chunk 89 optimal weight: 7.9990 overall best weight: 0.2952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.124032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084145 restraints weight = 16684.093| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.18 r_work: 0.3231 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9743 Z= 0.134 Angle : 0.533 15.390 13221 Z= 0.263 Chirality : 0.044 0.186 1473 Planarity : 0.004 0.037 1740 Dihedral : 4.887 53.887 1571 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.24 % Allowed : 10.95 % Favored : 87.81 % 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: -0.39 (0.25), residues: 1195 helix: -1.26 (0.60), residues: 74 sheet: -0.73 (0.46), residues: 143 loop : -0.06 (0.21), residues: 978 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 219 TYR 0.015 0.001 TYR A 523 ARG 0.006 0.000 ARG B 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6242.18 seconds wall clock time: 111 minutes 55.71 seconds (6715.71 seconds total)