Starting phenix.real_space_refine on Tue Feb 3 22:18:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n7d_49092/02_2026/9n7d_49092.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n7d_49092/02_2026/9n7d_49092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n7d_49092/02_2026/9n7d_49092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n7d_49092/02_2026/9n7d_49092.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n7d_49092/02_2026/9n7d_49092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n7d_49092/02_2026/9n7d_49092.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.071 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 41 5.16 5 C 4596 2.51 5 N 1184 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7246 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5502 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 671} Chain breaks: 1 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 25, 'ASP:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 175 Chain: "B" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1451 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 5, 'ASN:plan1': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 1.71, per 1000 atoms: 0.24 Number of scatterers: 7246 At special positions: 0 Unit cell: (77.0847, 93.1023, 138.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 41 16.00 O 1424 8.00 N 1184 7.00 C 4596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.02 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 413 " distance=2.03 Simple disulfide: pdb=" SG CYS B 431 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 530 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 801 " - " ASN A 90 " " NAG A 802 " - " ASN A 690 " " NAG A 803 " - " ASN A 82 " " NAG B 701 " - " ASN B 416 " " NAG B 702 " - " ASN B 493 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 432 " " NAG F 1 " - " ASN B 404 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 171.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 804 " - pdb=" NE2 HIS A 378 " 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 57.1% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 19 through 52 removed outlier: 3.545A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.545A pdb=" N SER A 106 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.627A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 3.593A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.886A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.587A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.664A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.903A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.608A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.575A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.579A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 465 removed outlier: 3.751A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.568A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.600A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.873A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.509A pdb=" N GLU A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 659 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 707 through 716 Processing helix chain 'B' and resid 391 through 397 removed outlier: 3.902A pdb=" N PHE B 395 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.511A pdb=" N PHE B 405 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.804A pdb=" N ALA B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 removed outlier: 5.030A pdb=" N SER B 460 " --> pdb=" O TYR B 457 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 463 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.813A pdb=" N SER B 535 " --> pdb=" O TYR B 532 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.880A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.503A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AA5, first strand: chain 'B' and resid 406 through 410 removed outlier: 7.641A pdb=" N THR B 483 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N CYS B 431 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG B 485 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B 429 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 487 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 406 through 410 Processing sheet with id=AA7, first strand: chain 'B' and resid 516 through 519 removed outlier: 6.760A pdb=" N THR B 555 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 508 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA B 553 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 543 " --> pdb=" O GLY B 556 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2237 1.34 - 1.47: 1959 1.47 - 1.59: 3070 1.59 - 1.72: 0 1.72 - 1.84: 66 Bond restraints: 7332 Sorted by residual: bond pdb=" N VAL A 132 " pdb=" CA VAL A 132 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.14e-02 7.69e+03 8.41e+00 bond pdb=" N PHE A 274 " pdb=" CA PHE A 274 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.06e+00 bond pdb=" N ASN A 137 " pdb=" CA ASN A 137 " ideal model delta sigma weight residual 1.462 1.488 -0.026 1.00e-02 1.00e+04 6.64e+00 bond pdb=" N ASP A 269 " pdb=" CA ASP A 269 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.29e-02 6.01e+03 6.63e+00 bond pdb=" N TRP A 271 " pdb=" CA TRP A 271 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.32e-02 5.74e+03 6.07e+00 ... (remaining 7327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 9777 1.40 - 2.80: 190 2.80 - 4.21: 24 4.21 - 5.61: 12 5.61 - 7.01: 1 Bond angle restraints: 10004 Sorted by residual: angle pdb=" CA ASP A 355 " pdb=" CB ASP A 355 " pdb=" CG ASP A 355 " ideal model delta sigma weight residual 112.60 117.10 -4.50 1.00e+00 1.00e+00 2.02e+01 angle pdb=" CA ASP A 269 " pdb=" CB ASP A 269 " pdb=" CG ASP A 269 " ideal model delta sigma weight residual 112.60 116.97 -4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" CA ASP A 269 " pdb=" C ASP A 269 " pdb=" O ASP A 269 " ideal model delta sigma weight residual 121.40 117.37 4.03 1.13e+00 7.83e-01 1.27e+01 angle pdb=" C ASP A 355 " pdb=" CA ASP A 355 " pdb=" CB ASP A 355 " ideal model delta sigma weight residual 110.78 115.31 -4.53 1.60e+00 3.91e-01 8.00e+00 angle pdb=" N VAL A 132 " pdb=" CA VAL A 132 " pdb=" C VAL A 132 " ideal model delta sigma weight residual 108.48 104.68 3.80 1.44e+00 4.82e-01 6.97e+00 ... (remaining 9999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 4183 17.15 - 34.29: 220 34.29 - 51.44: 50 51.44 - 68.58: 18 68.58 - 85.73: 4 Dihedral angle restraints: 4475 sinusoidal: 1821 harmonic: 2654 Sorted by residual: dihedral pdb=" CB CYS B 443 " pdb=" SG CYS B 443 " pdb=" SG CYS B 583 " pdb=" CB CYS B 583 " ideal model delta sinusoidal sigma weight residual 93.00 127.33 -34.33 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA SER A 254 " pdb=" C SER A 254 " pdb=" N TYR A 255 " pdb=" CA TYR A 255 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA CYS B 431 " pdb=" CB CYS B 431 " pdb=" SG CYS B 431 " pdb=" SG CYS B 484 " ideal model delta sinusoidal sigma weight residual -73.00 -10.27 -62.73 1 2.00e+01 2.50e-03 1.30e+01 ... (remaining 4472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 1122 0.215 - 0.430: 1 0.430 - 0.645: 0 0.645 - 0.860: 0 0.860 - 1.074: 1 Chirality restraints: 1124 Sorted by residual: chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CA VAL A 132 " pdb=" N VAL A 132 " pdb=" C VAL A 132 " pdb=" CB VAL A 132 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 1121 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 803 " 0.044 2.00e-02 2.50e+03 3.66e-02 1.67e+01 pdb=" C7 NAG A 803 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 803 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG A 803 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A 803 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 500 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " -0.196 9.50e-02 1.11e+02 8.78e-02 4.78e+00 pdb=" NE ARG A 273 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.006 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1843 2.81 - 3.33: 6517 3.33 - 3.85: 12224 3.85 - 4.38: 15188 4.38 - 4.90: 24445 Nonbonded interactions: 60217 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 804 " model vdw 2.281 2.230 nonbonded pdb=" OD1 ASP A 355 " pdb=" O HOH A 901 " model vdw 2.476 3.040 nonbonded pdb=" N ASP A 269 " pdb=" O ASP A 269 " model vdw 2.596 2.496 nonbonded pdb=" N ASN A 397 " pdb=" O ASN A 397 " model vdw 2.625 2.496 nonbonded pdb=" N ASP A 198 " pdb=" O ASP A 198 " model vdw 2.630 2.496 ... (remaining 60212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.350 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.003 0.036 7354 Z= 0.164 Angle : 0.543 13.950 10057 Z= 0.293 Chirality : 0.053 1.074 1124 Planarity : 0.005 0.088 1269 Dihedral : 11.617 85.728 2742 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.17 % Allowed : 5.40 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 889 helix: -0.21 (0.23), residues: 431 sheet: 1.25 (0.50), residues: 101 loop : -0.05 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.018 0.001 TYR A 385 PHE 0.010 0.001 PHE A 665 TRP 0.012 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7332) covalent geometry : angle 0.50984 (10004) SS BOND : bond 0.00453 ( 7) SS BOND : angle 1.79348 ( 14) hydrogen bonds : bond 0.25963 ( 361) hydrogen bonds : angle 6.74611 ( 1032) metal coordination : bond 0.00084 ( 2) link_BETA1-4 : bond 0.00397 ( 4) link_BETA1-4 : angle 1.09606 ( 12) link_NAG-ASN : bond 0.00375 ( 9) link_NAG-ASN : angle 3.34318 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.275 Fit side-chains REVERT: A 31 LYS cc_start: 0.8077 (ptpt) cc_final: 0.7758 (ptmm) REVERT: A 35 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: A 37 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: A 140 GLU cc_start: 0.8231 (tt0) cc_final: 0.7911 (tt0) REVERT: A 208 GLU cc_start: 0.8588 (tt0) cc_final: 0.8365 (tt0) REVERT: A 387 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8198 (mmtm) REVERT: A 435 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: A 514 ARG cc_start: 0.8670 (ptm160) cc_final: 0.8339 (ptp90) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.6688 time to fit residues: 64.4295 Evaluate side-chains 84 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 134 ASN A 218 ASN B 550 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113390 restraints weight = 7073.879| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.56 r_work: 0.3184 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7354 Z= 0.140 Angle : 0.574 10.327 10057 Z= 0.303 Chirality : 0.046 0.342 1124 Planarity : 0.005 0.048 1269 Dihedral : 6.068 53.573 1263 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.92 % Allowed : 6.28 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.28), residues: 889 helix: 1.09 (0.25), residues: 442 sheet: 1.21 (0.50), residues: 100 loop : 0.02 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 407 TYR 0.014 0.001 TYR A 385 PHE 0.010 0.002 PHE A 314 TRP 0.015 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7332) covalent geometry : angle 0.55013 (10004) SS BOND : bond 0.01005 ( 7) SS BOND : angle 2.76495 ( 14) hydrogen bonds : bond 0.06773 ( 361) hydrogen bonds : angle 4.67088 ( 1032) metal coordination : bond 0.00052 ( 2) link_BETA1-4 : bond 0.00660 ( 4) link_BETA1-4 : angle 1.29913 ( 12) link_NAG-ASN : bond 0.00592 ( 9) link_NAG-ASN : angle 2.42295 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7919 (ptpt) cc_final: 0.7562 (pttp) REVERT: A 35 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: A 37 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: A 60 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6691 (tm130) REVERT: A 140 GLU cc_start: 0.8016 (tt0) cc_final: 0.7772 (tt0) REVERT: A 270 MET cc_start: 0.8911 (tpp) cc_final: 0.8513 (tpt) REVERT: A 387 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8232 (mmtm) REVERT: A 435 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: A 514 ARG cc_start: 0.8651 (ptm160) cc_final: 0.8381 (ptp90) REVERT: A 531 GLN cc_start: 0.8247 (tt0) cc_final: 0.8003 (tt0) REVERT: B 417 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7749 (mm) outliers start: 20 outliers final: 8 residues processed: 95 average time/residue: 0.7056 time to fit residues: 70.2069 Evaluate side-chains 96 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114161 restraints weight = 7046.208| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.55 r_work: 0.3194 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7354 Z= 0.126 Angle : 0.537 8.895 10057 Z= 0.279 Chirality : 0.044 0.284 1124 Planarity : 0.004 0.043 1269 Dihedral : 5.896 52.399 1263 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.92 % Allowed : 7.45 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.28), residues: 889 helix: 1.59 (0.25), residues: 442 sheet: 1.01 (0.49), residues: 100 loop : 0.05 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 407 TYR 0.013 0.001 TYR A 385 PHE 0.010 0.001 PHE A 523 TRP 0.016 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7332) covalent geometry : angle 0.51102 (10004) SS BOND : bond 0.01139 ( 7) SS BOND : angle 2.95419 ( 14) hydrogen bonds : bond 0.05873 ( 361) hydrogen bonds : angle 4.28625 ( 1032) metal coordination : bond 0.00052 ( 2) link_BETA1-4 : bond 0.00523 ( 4) link_BETA1-4 : angle 1.24375 ( 12) link_NAG-ASN : bond 0.00459 ( 9) link_NAG-ASN : angle 2.28974 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.178 Fit side-chains REVERT: A 31 LYS cc_start: 0.7916 (ptpt) cc_final: 0.7537 (pttp) REVERT: A 35 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: A 37 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: A 60 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6549 (tm130) REVERT: A 335 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6668 (tm-30) REVERT: A 387 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8280 (mmtm) REVERT: A 435 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: A 514 ARG cc_start: 0.8683 (ptm160) cc_final: 0.8430 (ptp90) REVERT: A 531 GLN cc_start: 0.8219 (tt0) cc_final: 0.7960 (tt0) REVERT: B 417 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7817 (mm) outliers start: 20 outliers final: 7 residues processed: 91 average time/residue: 0.6635 time to fit residues: 63.1842 Evaluate side-chains 94 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 218 ASN B 550 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112331 restraints weight = 7162.451| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.56 r_work: 0.3170 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 7354 Z= 0.154 Angle : 0.576 11.503 10057 Z= 0.302 Chirality : 0.046 0.257 1124 Planarity : 0.005 0.041 1269 Dihedral : 6.111 54.924 1263 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.92 % Allowed : 8.18 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.28), residues: 889 helix: 1.61 (0.25), residues: 442 sheet: 1.08 (0.53), residues: 89 loop : -0.12 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 407 TYR 0.016 0.002 TYR A 385 PHE 0.014 0.002 PHE A 523 TRP 0.017 0.002 TRP A 478 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7332) covalent geometry : angle 0.54817 (10004) SS BOND : bond 0.01174 ( 7) SS BOND : angle 3.52810 ( 14) hydrogen bonds : bond 0.06313 ( 361) hydrogen bonds : angle 4.25872 ( 1032) metal coordination : bond 0.00113 ( 2) link_BETA1-4 : bond 0.00607 ( 4) link_BETA1-4 : angle 1.22136 ( 12) link_NAG-ASN : bond 0.00409 ( 9) link_NAG-ASN : angle 2.23893 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7998 (ptpt) cc_final: 0.7613 (pttp) REVERT: A 35 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: A 37 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: A 60 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6568 (tm130) REVERT: A 305 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: A 335 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: A 387 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8285 (mmtm) REVERT: A 435 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: A 514 ARG cc_start: 0.8707 (ptm160) cc_final: 0.8453 (ptp90) REVERT: A 531 GLN cc_start: 0.8228 (tt0) cc_final: 0.7980 (tt0) REVERT: A 597 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: B 417 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7797 (mm) outliers start: 20 outliers final: 7 residues processed: 92 average time/residue: 0.6884 time to fit residues: 66.3326 Evaluate side-chains 97 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 466 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113272 restraints weight = 7059.298| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.58 r_work: 0.3192 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7354 Z= 0.126 Angle : 0.533 9.839 10057 Z= 0.279 Chirality : 0.044 0.235 1124 Planarity : 0.004 0.041 1269 Dihedral : 5.967 53.863 1263 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.77 % Allowed : 8.47 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.28), residues: 889 helix: 1.74 (0.25), residues: 442 sheet: 0.96 (0.49), residues: 100 loop : -0.01 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 407 TYR 0.012 0.001 TYR A 385 PHE 0.011 0.001 PHE A 523 TRP 0.016 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7332) covalent geometry : angle 0.50821 (10004) SS BOND : bond 0.01093 ( 7) SS BOND : angle 3.05447 ( 14) hydrogen bonds : bond 0.05457 ( 361) hydrogen bonds : angle 4.16325 ( 1032) metal coordination : bond 0.00105 ( 2) link_BETA1-4 : bond 0.00564 ( 4) link_BETA1-4 : angle 1.16292 ( 12) link_NAG-ASN : bond 0.00397 ( 9) link_NAG-ASN : angle 2.12806 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7618 (pttp) REVERT: A 35 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: A 37 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: A 335 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: A 387 LYS cc_start: 0.8632 (mptm) cc_final: 0.8316 (mmtm) REVERT: A 435 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: A 514 ARG cc_start: 0.8703 (ptm160) cc_final: 0.8447 (ptp90) REVERT: A 531 GLN cc_start: 0.8209 (tt0) cc_final: 0.7953 (tt0) REVERT: A 597 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: A 621 ARG cc_start: 0.7870 (ttm170) cc_final: 0.7529 (ttm110) REVERT: B 417 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7824 (mm) outliers start: 19 outliers final: 8 residues processed: 92 average time/residue: 0.6556 time to fit residues: 63.2135 Evaluate side-chains 95 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 541 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 63 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113271 restraints weight = 7077.973| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.59 r_work: 0.3194 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7354 Z= 0.125 Angle : 0.526 8.997 10057 Z= 0.275 Chirality : 0.043 0.223 1124 Planarity : 0.004 0.041 1269 Dihedral : 5.738 53.797 1259 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.92 % Allowed : 8.76 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.28), residues: 889 helix: 1.76 (0.25), residues: 444 sheet: 0.94 (0.49), residues: 100 loop : 0.03 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 407 TYR 0.013 0.001 TYR A 385 PHE 0.012 0.001 PHE A 523 TRP 0.016 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7332) covalent geometry : angle 0.50338 (10004) SS BOND : bond 0.00972 ( 7) SS BOND : angle 2.85723 ( 14) hydrogen bonds : bond 0.05366 ( 361) hydrogen bonds : angle 4.07812 ( 1032) metal coordination : bond 0.00091 ( 2) link_BETA1-4 : bond 0.00559 ( 4) link_BETA1-4 : angle 1.12863 ( 12) link_NAG-ASN : bond 0.00394 ( 9) link_NAG-ASN : angle 2.08077 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8002 (ptpt) cc_final: 0.7606 (pttp) REVERT: A 35 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: A 37 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7901 (mm-30) REVERT: A 335 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: A 387 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8274 (mmtm) REVERT: A 435 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: A 531 GLN cc_start: 0.8183 (tt0) cc_final: 0.7926 (tt0) REVERT: A 597 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: A 621 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7504 (ttm110) REVERT: B 417 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7805 (mm) outliers start: 20 outliers final: 9 residues processed: 94 average time/residue: 0.5881 time to fit residues: 58.0457 Evaluate side-chains 94 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 541 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 0.0060 chunk 11 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.114675 restraints weight = 7147.249| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.59 r_work: 0.3211 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 7354 Z= 0.112 Angle : 0.510 11.616 10057 Z= 0.266 Chirality : 0.042 0.219 1124 Planarity : 0.004 0.041 1269 Dihedral : 5.597 52.721 1259 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.34 % Allowed : 9.05 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.28), residues: 889 helix: 1.87 (0.25), residues: 444 sheet: 0.92 (0.49), residues: 100 loop : 0.09 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 407 TYR 0.013 0.001 TYR A 50 PHE 0.010 0.001 PHE A 684 TRP 0.015 0.001 TRP A 478 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7332) covalent geometry : angle 0.48182 (10004) SS BOND : bond 0.01103 ( 7) SS BOND : angle 3.53676 ( 14) hydrogen bonds : bond 0.04879 ( 361) hydrogen bonds : angle 4.02134 ( 1032) metal coordination : bond 0.00082 ( 2) link_BETA1-4 : bond 0.00472 ( 4) link_BETA1-4 : angle 1.08448 ( 12) link_NAG-ASN : bond 0.00383 ( 9) link_NAG-ASN : angle 1.99453 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7975 (ptpt) cc_final: 0.7594 (pttp) REVERT: A 35 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: A 37 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: A 335 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6589 (tm-30) REVERT: A 387 LYS cc_start: 0.8581 (mptm) cc_final: 0.8266 (mmtm) REVERT: A 435 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: A 531 GLN cc_start: 0.8163 (tt0) cc_final: 0.7912 (tt0) REVERT: A 597 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: A 621 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7614 (ttm110) REVERT: B 417 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7817 (mm) outliers start: 16 outliers final: 7 residues processed: 88 average time/residue: 0.6130 time to fit residues: 56.5502 Evaluate side-chains 89 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 541 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 218 ASN B 550 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113966 restraints weight = 7168.691| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.57 r_work: 0.3199 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7354 Z= 0.129 Angle : 0.537 11.141 10057 Z= 0.282 Chirality : 0.044 0.227 1124 Planarity : 0.004 0.041 1269 Dihedral : 5.710 54.516 1259 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.19 % Allowed : 9.34 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.28), residues: 889 helix: 1.83 (0.25), residues: 444 sheet: 0.92 (0.49), residues: 100 loop : 0.01 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.018 0.001 TYR A 50 PHE 0.013 0.001 PHE A 523 TRP 0.016 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7332) covalent geometry : angle 0.51034 (10004) SS BOND : bond 0.01179 ( 7) SS BOND : angle 3.45287 ( 14) hydrogen bonds : bond 0.05359 ( 361) hydrogen bonds : angle 4.05318 ( 1032) metal coordination : bond 0.00107 ( 2) link_BETA1-4 : bond 0.00552 ( 4) link_BETA1-4 : angle 1.06508 ( 12) link_NAG-ASN : bond 0.00391 ( 9) link_NAG-ASN : angle 2.05000 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8026 (ptpt) cc_final: 0.7611 (pttp) REVERT: A 35 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: A 37 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: A 335 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: A 387 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8279 (mmtm) REVERT: A 435 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: A 531 GLN cc_start: 0.8156 (tt0) cc_final: 0.7904 (tt0) REVERT: A 597 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 621 ARG cc_start: 0.7872 (ttm170) cc_final: 0.7642 (ttm110) REVERT: B 407 ARG cc_start: 0.8369 (tpp-160) cc_final: 0.8137 (mtt-85) REVERT: B 417 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7850 (mm) outliers start: 15 outliers final: 7 residues processed: 84 average time/residue: 0.7303 time to fit residues: 64.2289 Evaluate side-chains 89 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 541 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 6 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 218 ASN B 550 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112854 restraints weight = 6981.084| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.54 r_work: 0.3187 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 7354 Z= 0.145 Angle : 0.563 10.745 10057 Z= 0.296 Chirality : 0.045 0.231 1124 Planarity : 0.004 0.040 1269 Dihedral : 5.863 57.027 1259 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.34 % Allowed : 9.34 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.28), residues: 889 helix: 1.79 (0.25), residues: 442 sheet: 0.98 (0.50), residues: 95 loop : -0.09 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.021 0.002 TYR A 50 PHE 0.014 0.002 PHE A 523 TRP 0.015 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7332) covalent geometry : angle 0.53742 (10004) SS BOND : bond 0.01149 ( 7) SS BOND : angle 3.36116 ( 14) hydrogen bonds : bond 0.05843 ( 361) hydrogen bonds : angle 4.10502 ( 1032) metal coordination : bond 0.00094 ( 2) link_BETA1-4 : bond 0.00553 ( 4) link_BETA1-4 : angle 1.06711 ( 12) link_NAG-ASN : bond 0.00413 ( 9) link_NAG-ASN : angle 2.15109 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8083 (ptpt) cc_final: 0.7638 (pttp) REVERT: A 35 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: A 37 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7925 (mm-30) REVERT: A 335 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: A 387 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8269 (mmtm) REVERT: A 435 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: A 514 ARG cc_start: 0.8681 (ptm160) cc_final: 0.8420 (ptp90) REVERT: A 531 GLN cc_start: 0.8165 (tt0) cc_final: 0.7923 (tt0) REVERT: A 597 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: A 621 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7678 (ttm110) REVERT: B 417 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7874 (mm) outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 0.7100 time to fit residues: 65.2681 Evaluate side-chains 93 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 541 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 218 ASN B 550 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113304 restraints weight = 7075.609| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.56 r_work: 0.3190 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7354 Z= 0.136 Angle : 0.558 12.076 10057 Z= 0.292 Chirality : 0.044 0.219 1124 Planarity : 0.004 0.040 1269 Dihedral : 5.830 57.003 1259 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.48 % Allowed : 9.49 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.28), residues: 889 helix: 1.76 (0.25), residues: 444 sheet: 1.00 (0.50), residues: 95 loop : -0.06 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 697 TYR 0.021 0.002 TYR A 50 PHE 0.013 0.001 PHE A 523 TRP 0.015 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7332) covalent geometry : angle 0.52991 (10004) SS BOND : bond 0.01227 ( 7) SS BOND : angle 3.69550 ( 14) hydrogen bonds : bond 0.05604 ( 361) hydrogen bonds : angle 4.10035 ( 1032) metal coordination : bond 0.00120 ( 2) link_BETA1-4 : bond 0.00548 ( 4) link_BETA1-4 : angle 1.05154 ( 12) link_NAG-ASN : bond 0.00416 ( 9) link_NAG-ASN : angle 2.10478 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8095 (ptpt) cc_final: 0.7649 (pttp) REVERT: A 35 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: A 37 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: A 63 ASN cc_start: 0.8241 (m-40) cc_final: 0.7962 (m-40) REVERT: A 335 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: A 387 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8266 (mmtm) REVERT: A 435 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: A 514 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8412 (ptp90) REVERT: A 531 GLN cc_start: 0.8187 (tt0) cc_final: 0.7940 (tt0) REVERT: A 597 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: A 621 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7698 (ttm110) REVERT: B 417 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7865 (mm) outliers start: 17 outliers final: 9 residues processed: 88 average time/residue: 0.7008 time to fit residues: 64.4811 Evaluate side-chains 93 residues out of total 799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 541 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 218 ASN B 550 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113871 restraints weight = 7034.120| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.56 r_work: 0.3202 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7354 Z= 0.129 Angle : 0.545 11.863 10057 Z= 0.284 Chirality : 0.043 0.216 1124 Planarity : 0.004 0.041 1269 Dihedral : 5.763 56.155 1259 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.48 % Allowed : 9.49 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.28), residues: 889 helix: 1.80 (0.25), residues: 444 sheet: 0.95 (0.49), residues: 95 loop : -0.04 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 697 TYR 0.018 0.001 TYR A 50 PHE 0.012 0.001 PHE A 523 TRP 0.015 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7332) covalent geometry : angle 0.51669 (10004) SS BOND : bond 0.01184 ( 7) SS BOND : angle 3.61113 ( 14) hydrogen bonds : bond 0.05353 ( 361) hydrogen bonds : angle 4.06332 ( 1032) metal coordination : bond 0.00112 ( 2) link_BETA1-4 : bond 0.00543 ( 4) link_BETA1-4 : angle 1.04366 ( 12) link_NAG-ASN : bond 0.00403 ( 9) link_NAG-ASN : angle 2.08287 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.66 seconds wall clock time: 48 minutes 38.87 seconds (2918.87 seconds total)