Starting phenix.real_space_refine on Fri Sep 11 14:48:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xi6_66898/09_2026/9xi6_66898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xi6_66898/09_2026/9xi6_66898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xi6_66898/09_2026/9xi6_66898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xi6_66898/09_2026/9xi6_66898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xi6_66898/09_2026/9xi6_66898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xi6_66898/09_2026/9xi6_66898.map" } resolution = 2.6 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= 0.031 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 47 5.16 5 C 6154 2.51 5 N 1601 2.21 5 O 1863 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9666 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4864 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1540 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "H" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1639 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1566 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.95, per 1000 atoms: 0.20 Number of scatterers: 9666 At special positions: 0 Unit cell: (77.592, 137.616, 135.42, 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 47 16.00 O 1863 8.00 N 1601 7.00 C 6154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " 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 NAG-ASN " NAG A 902 " - " ASN A 53 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 546 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 365.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 18 sheets defined 38.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.653A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.728A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.743A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.763A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.536A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.487A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) 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 498 through 502 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.604A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.297A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.812A 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 Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.681A pdb=" N ASP A 615 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.810A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 371 removed outlier: 4.203A pdb=" N PHE E 371 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.390A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.572A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.802A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 133 removed outlier: 3.706A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA L 132 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 193 removed outlier: 3.643A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS L 193 " --> pdb=" O GLN L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.798A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.251A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.532A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.569A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 466 through 467 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.235A pdb=" N ILE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 57 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.658A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.582A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 162 through 165 Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.385A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.671A pdb=" N LEU L 140 " --> pdb=" O THR L 121 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER L 181 " --> pdb=" O CYS L 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.671A pdb=" N LEU L 140 " --> pdb=" O THR L 121 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP L 143 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 150 through 155 removed outlier: 3.604A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL L 211 " --> pdb=" O TYR L 196 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS L 198 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1206 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: 1.43 Time building geometry restraints manager: 0.95 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: 2546 1.33 - 1.46: 2677 1.46 - 1.58: 4633 1.58 - 1.71: 0 1.71 - 1.84: 70 Bond restraints: 9926 Sorted by residual: bond pdb=" N GLN A 472 " pdb=" CA GLN A 472 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.00e-02 1.00e+04 1.00e+01 bond pdb=" N LEU A 91 " pdb=" CA LEU A 91 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.19e+00 bond pdb=" N VAL H 18 " pdb=" CA VAL H 18 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.43e+00 bond pdb=" N ILE A 151 " pdb=" CA ILE A 151 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.32e+00 bond pdb=" N CYS E 432 " pdb=" CA CYS E 432 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.91e+00 ... (remaining 9921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 13194 2.20 - 4.41: 283 4.41 - 6.61: 32 6.61 - 8.81: 5 8.81 - 11.02: 3 Bond angle restraints: 13517 Sorted by residual: angle pdb=" O GLY L 112 " pdb=" C GLY L 112 " pdb=" N GLN L 113 " ideal model delta sigma weight residual 122.70 111.68 11.02 1.30e+00 5.92e-01 7.18e+01 angle pdb=" C ASN A 90 " pdb=" CA ASN A 90 " pdb=" CB ASN A 90 " ideal model delta sigma weight residual 109.71 116.59 -6.88 1.83e+00 2.99e-01 1.41e+01 angle pdb=" N ILE A 259 " pdb=" CA ILE A 259 " pdb=" C ILE A 259 " ideal model delta sigma weight residual 112.96 109.26 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" N LEU A 278 " pdb=" CA LEU A 278 " pdb=" C LEU A 278 " ideal model delta sigma weight residual 112.59 108.09 4.50 1.22e+00 6.72e-01 1.36e+01 angle pdb=" N LEU A 142 " pdb=" CA LEU A 142 " pdb=" C LEU A 142 " ideal model delta sigma weight residual 111.90 116.56 -4.66 1.32e+00 5.74e-01 1.25e+01 ... (remaining 13512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5065 17.43 - 34.86: 606 34.86 - 52.30: 192 52.30 - 69.73: 38 69.73 - 87.16: 23 Dihedral angle restraints: 5924 sinusoidal: 2361 harmonic: 3563 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -145.21 59.21 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -49.79 -36.21 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CA ALA A 396 " pdb=" C ALA A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1404 0.105 - 0.210: 65 0.210 - 0.316: 0 0.316 - 0.421: 0 0.421 - 0.526: 1 Chirality restraints: 1470 Sorted by residual: chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CA VAL E 433 " pdb=" N VAL E 433 " pdb=" C VAL E 433 " pdb=" CB VAL E 433 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA LEU A 278 " pdb=" N LEU A 278 " pdb=" C LEU A 278 " pdb=" CB LEU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.65e-01 ... (remaining 1467 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 112 " 0.063 2.00e-02 2.50e+03 1.18e-01 1.38e+02 pdb=" C GLY L 112 " -0.203 2.00e-02 2.50e+03 pdb=" O GLY L 112 " 0.076 2.00e-02 2.50e+03 pdb=" N GLN L 113 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 89 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLN A 89 " 0.057 2.00e-02 2.50e+03 pdb=" O GLN A 89 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 90 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 500 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " -0.030 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 233 2.69 - 3.25: 8831 3.25 - 3.80: 16038 3.80 - 4.35: 21195 4.35 - 4.90: 34613 Nonbonded interactions: 80910 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.143 2.230 nonbonded pdb=" OG SER L 27 " pdb=" OD1 ASP L 94 " model vdw 2.231 3.040 nonbonded pdb=" OG SER A 331 " pdb=" O ILE A 358 " model vdw 2.245 3.040 nonbonded pdb=" OE2 GLU E 471 " pdb=" OH TYR H 32 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP A 543 " pdb=" OG SER A 545 " model vdw 2.342 3.040 ... (remaining 80905 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 8.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.150 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:8.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.004 0.048 9943 Z= 0.232 Angle : 0.774 12.117 13551 Z= 0.441 Chirality : 0.051 0.526 1470 Planarity : 0.006 0.118 1741 Dihedral : 17.362 87.162 3613 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.76 % Allowed : 24.52 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.63 (0.23), residues: 1216 helix: -0.19 (0.24), residues: 405 sheet: 0.52 (0.33), residues: 254 loop : -0.97 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 306 TYR 0.017 0.002 TYR A 385 PHE 0.017 0.002 PHE A 523 TRP 0.021 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.23 ( 9926) covalent geometry : angle 0.75575 / 0.44 (13517) SS BOND : bond 0.00553 / 0.36 ( 11) SS BOND : angle 1.78996 / 1.01 ( 22) hydrogen bonds : bond 0.19768 / 12.67 ( 427) hydrogen bonds : angle 7.47133 / 5.41 ( 1206) metal coordination : bond 0.00189 / 0.09 ( 2) link_NAG-ASN : bond 0.01500 / 0.71 ( 4) link_NAG-ASN : angle 5.20822 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 117 ASN cc_start: 0.7270 (t0) cc_final: 0.7040 (t160) REVERT: A 435 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6863 (tt0) REVERT: A 476 LYS cc_start: 0.7643 (tptt) cc_final: 0.7355 (tppt) REVERT: E 450 ASN cc_start: 0.8294 (m-40) cc_final: 0.8091 (m110) REVERT: E 458 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7787 (mtmp) REVERT: L 83 GLU cc_start: 0.7804 (pm20) cc_final: 0.7413 (pm20) outliers start: 8 outliers final: 2 residues processed: 167 average time/residue: 0.6226 time to fit residues: 110.9191 Evaluate side-chains 116 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain L residue 193 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 340 GLN A 531 GLN L 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.187996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146609 restraints weight = 9252.241| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.43 r_work: 0.3350 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9943 Z= 0.169 Angle : 0.616 9.095 13551 Z= 0.320 Chirality : 0.045 0.205 1470 Planarity : 0.004 0.042 1741 Dihedral : 5.262 48.093 1411 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.68 % Allowed : 20.42 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.18 (0.23), residues: 1216 helix: 0.75 (0.25), residues: 414 sheet: 0.81 (0.32), residues: 260 loop : -0.68 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 454 TYR 0.019 0.002 TYR A 385 PHE 0.021 0.002 PHE H 111 TRP 0.013 0.001 TRP A 165 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 9926) covalent geometry : angle 0.60177 / 0.32 (13517) SS BOND : bond 0.00467 / 0.28 ( 11) SS BOND : angle 1.53193 / 0.84 ( 22) hydrogen bonds : bond 0.05693 / 3.64 ( 427) hydrogen bonds : angle 5.30505 / 3.84 ( 1206) metal coordination : bond 0.00487 / 0.23 ( 2) link_NAG-ASN : bond 0.01137 / 0.54 ( 4) link_NAG-ASN : angle 4.07069 / 2.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7749 (mm110) cc_final: 0.7512 (mm-40) REVERT: A 86 GLN cc_start: 0.7964 (pm20) cc_final: 0.7645 (pm20) REVERT: A 102 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7222 (mm-40) REVERT: A 117 ASN cc_start: 0.7577 (t0) cc_final: 0.7371 (t160) REVERT: A 166 GLU cc_start: 0.7150 (tp30) cc_final: 0.6922 (mm-30) REVERT: A 182 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: A 270 MET cc_start: 0.7674 (tpt) cc_final: 0.7348 (tpt) REVERT: A 305 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: A 376 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8397 (ttm) REVERT: A 416 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7034 (ptpt) REVERT: A 435 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7087 (tt0) REVERT: A 476 LYS cc_start: 0.7610 (tptt) cc_final: 0.7304 (tppt) REVERT: A 483 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: A 531 GLN cc_start: 0.7853 (tt0) cc_final: 0.7212 (mt0) REVERT: E 340 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7125 (mp0) REVERT: E 450 ASN cc_start: 0.8439 (m-40) cc_final: 0.8144 (m110) REVERT: E 458 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7826 (mtmt) REVERT: E 471 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: H 87 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7324 (mtm-85) REVERT: L 17 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7589 (ttt180) REVERT: L 41 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7998 (mt) REVERT: L 83 GLU cc_start: 0.8239 (pm20) cc_final: 0.7828 (pm20) outliers start: 49 outliers final: 13 residues processed: 160 average time/residue: 0.6039 time to fit residues: 103.2050 Evaluate side-chains 131 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 193 HIS Chi-restraints excluded: chain L residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 535 HIS E 506 GLN H 6 GLN H 39 GLN L 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.185724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144568 restraints weight = 9236.777| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.54 r_work: 0.3334 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9943 Z= 0.143 Angle : 0.568 9.347 13551 Z= 0.293 Chirality : 0.044 0.294 1470 Planarity : 0.004 0.039 1741 Dihedral : 5.029 50.270 1411 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.34 % Allowed : 19.94 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.54 (0.24), residues: 1216 helix: 1.23 (0.25), residues: 410 sheet: 0.83 (0.32), residues: 257 loop : -0.50 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 454 TYR 0.018 0.001 TYR A 385 PHE 0.018 0.002 PHE H 133 TRP 0.012 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9926) covalent geometry : angle 0.55465 / 0.29 (13517) SS BOND : bond 0.00417 / 0.25 ( 11) SS BOND : angle 1.41617 / 0.78 ( 22) hydrogen bonds : bond 0.05371 / 3.44 ( 427) hydrogen bonds : angle 5.02010 / 3.62 ( 1206) metal coordination : bond 0.00240 / 0.12 ( 2) link_NAG-ASN : bond 0.00738 / 0.35 ( 4) link_NAG-ASN : angle 3.75871 / 2.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: A 60 GLN cc_start: 0.7958 (mm110) cc_final: 0.7743 (mm-40) REVERT: A 86 GLN cc_start: 0.7955 (pm20) cc_final: 0.7663 (pm20) REVERT: A 102 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7149 (mm-40) REVERT: A 117 ASN cc_start: 0.7646 (t0) cc_final: 0.7419 (t160) REVERT: A 166 GLU cc_start: 0.6967 (tp30) cc_final: 0.6734 (mm-30) REVERT: A 182 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6179 (mp0) REVERT: A 224 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7088 (mm-30) REVERT: A 270 MET cc_start: 0.7790 (tpt) cc_final: 0.7423 (tpt) REVERT: A 299 ASP cc_start: 0.7596 (m-30) cc_final: 0.7343 (m-30) REVERT: A 376 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8559 (ttm) REVERT: A 416 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.6902 (ptpt) REVERT: A 435 GLU cc_start: 0.7685 (mt-10) cc_final: 0.6960 (tt0) REVERT: A 475 LYS cc_start: 0.8162 (tmtm) cc_final: 0.7910 (tmtm) REVERT: A 476 LYS cc_start: 0.7612 (tptt) cc_final: 0.7210 (tppt) REVERT: A 483 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: E 450 ASN cc_start: 0.8455 (m-40) cc_final: 0.8159 (m110) REVERT: E 458 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7820 (mtmt) REVERT: E 471 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: H 4 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8010 (pp) REVERT: H 82 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: H 100 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7724 (tpp-160) REVERT: L 83 GLU cc_start: 0.8154 (pm20) cc_final: 0.7808 (pm20) outliers start: 56 outliers final: 14 residues processed: 153 average time/residue: 0.6125 time to fit residues: 100.1802 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 193 HIS Chi-restraints excluded: chain L residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.184827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145108 restraints weight = 9283.013| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.98 r_work: 0.3310 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9943 Z= 0.137 Angle : 0.552 8.761 13551 Z= 0.285 Chirality : 0.044 0.307 1470 Planarity : 0.004 0.039 1741 Dihedral : 4.907 47.270 1411 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.39 % Allowed : 20.61 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.70 (0.24), residues: 1216 helix: 1.40 (0.25), residues: 410 sheet: 0.85 (0.32), residues: 256 loop : -0.39 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.018 0.001 TYR A 385 PHE 0.019 0.002 PHE H 133 TRP 0.011 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 9926) covalent geometry : angle 0.53929 / 0.28 (13517) SS BOND : bond 0.00464 / 0.29 ( 11) SS BOND : angle 1.57858 / 0.88 ( 22) hydrogen bonds : bond 0.05136 / 3.27 ( 427) hydrogen bonds : angle 4.89305 / 3.54 ( 1206) metal coordination : bond 0.00295 / 0.14 ( 2) link_NAG-ASN : bond 0.00651 / 0.31 ( 4) link_NAG-ASN : angle 3.50238 / 1.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7214 (mt-10) REVERT: A 56 GLU cc_start: 0.6461 (mm-30) cc_final: 0.6108 (mm-30) REVERT: A 60 GLN cc_start: 0.8093 (mm110) cc_final: 0.7858 (mm-40) REVERT: A 86 GLN cc_start: 0.8002 (pm20) cc_final: 0.7757 (pm20) REVERT: A 102 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7159 (mm-40) REVERT: A 117 ASN cc_start: 0.7659 (t0) cc_final: 0.7425 (t160) REVERT: A 224 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7137 (mm-30) REVERT: A 476 LYS cc_start: 0.7577 (tptt) cc_final: 0.7307 (tppt) REVERT: A 483 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: E 450 ASN cc_start: 0.8494 (m-40) cc_final: 0.8180 (m110) REVERT: E 458 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7867 (mtmt) REVERT: E 471 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: H 4 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7986 (pp) REVERT: H 87 ARG cc_start: 0.7881 (mpt180) cc_final: 0.7663 (mpt180) REVERT: H 100 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7651 (tpp-160) REVERT: L 63 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7704 (mtp-110) outliers start: 46 outliers final: 16 residues processed: 147 average time/residue: 0.6277 time to fit residues: 98.7427 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 193 HIS Chi-restraints excluded: chain L residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 0.0030 chunk 2 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 388 ASN L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.185125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.143399 restraints weight = 9306.883| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.48 r_work: 0.3330 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9943 Z= 0.124 Angle : 0.543 8.146 13551 Z= 0.277 Chirality : 0.043 0.297 1470 Planarity : 0.004 0.042 1741 Dihedral : 4.535 36.098 1408 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.72 % Allowed : 21.66 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.84 (0.24), residues: 1216 helix: 1.59 (0.25), residues: 409 sheet: 0.89 (0.32), residues: 247 loop : -0.32 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 357 TYR 0.018 0.001 TYR A 385 PHE 0.015 0.001 PHE A 523 TRP 0.011 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9926) covalent geometry : angle 0.53149 / 0.27 (13517) SS BOND : bond 0.00404 / 0.26 ( 11) SS BOND : angle 1.27893 / 0.71 ( 22) hydrogen bonds : bond 0.04888 / 3.12 ( 427) hydrogen bonds : angle 4.77722 / 3.46 ( 1206) metal coordination : bond 0.00226 / 0.11 ( 2) link_NAG-ASN : bond 0.00580 / 0.27 ( 4) link_NAG-ASN : angle 3.38508 / 1.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: A 56 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6004 (mm-30) REVERT: A 60 GLN cc_start: 0.8045 (mm110) cc_final: 0.7791 (mm-40) REVERT: A 86 GLN cc_start: 0.7985 (pm20) cc_final: 0.7749 (pm20) REVERT: A 102 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7141 (mm-40) REVERT: A 117 ASN cc_start: 0.7624 (t0) cc_final: 0.7386 (t160) REVERT: A 182 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6098 (mp0) REVERT: A 224 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7042 (mm-30) REVERT: A 270 MET cc_start: 0.7778 (tpt) cc_final: 0.7484 (tpt) REVERT: A 299 ASP cc_start: 0.7526 (m-30) cc_final: 0.7243 (m-30) REVERT: A 305 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7714 (mm-40) REVERT: A 416 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7132 (ptpt) REVERT: A 476 LYS cc_start: 0.7553 (tptt) cc_final: 0.7253 (tppt) REVERT: A 483 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: E 450 ASN cc_start: 0.8449 (m-40) cc_final: 0.8119 (m110) REVERT: E 458 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7838 (mtmt) REVERT: E 471 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: H 4 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7915 (pp) REVERT: H 82 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: H 87 ARG cc_start: 0.7809 (mpt180) cc_final: 0.7546 (mtt180) REVERT: H 100 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7590 (tpp-160) REVERT: L 63 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7721 (mtp-110) REVERT: L 83 GLU cc_start: 0.8275 (pm20) cc_final: 0.7951 (pm20) REVERT: L 180 SER cc_start: 0.8169 (t) cc_final: 0.7790 (p) outliers start: 39 outliers final: 15 residues processed: 140 average time/residue: 0.6296 time to fit residues: 94.4379 Evaluate side-chains 132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 193 HIS Chi-restraints excluded: chain L residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.182296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139853 restraints weight = 9239.527| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.33 r_work: 0.3269 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9943 Z= 0.160 Angle : 0.596 9.396 13551 Z= 0.307 Chirality : 0.046 0.303 1470 Planarity : 0.004 0.044 1741 Dihedral : 4.764 36.095 1408 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.87 % Allowed : 20.99 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.79 (0.24), residues: 1216 helix: 1.55 (0.25), residues: 408 sheet: 0.78 (0.32), residues: 252 loop : -0.32 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 357 TYR 0.017 0.002 TYR A 385 PHE 0.019 0.002 PHE A 523 TRP 0.011 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9926) covalent geometry : angle 0.58405 / 0.30 (13517) SS BOND : bond 0.01001 / 0.79 ( 11) SS BOND : angle 1.76847 / 0.98 ( 22) hydrogen bonds : bond 0.05469 / 3.48 ( 427) hydrogen bonds : angle 4.87987 / 3.54 ( 1206) metal coordination : bond 0.00406 / 0.19 ( 2) link_NAG-ASN : bond 0.00520 / 0.24 ( 4) link_NAG-ASN : angle 3.41372 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: A 56 GLU cc_start: 0.6567 (mm-30) cc_final: 0.6120 (mm-30) REVERT: A 60 GLN cc_start: 0.8100 (mm110) cc_final: 0.7881 (mm-40) REVERT: A 86 GLN cc_start: 0.8066 (pm20) cc_final: 0.7853 (pm20) REVERT: A 102 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7275 (mm-40) REVERT: A 117 ASN cc_start: 0.7718 (t0) cc_final: 0.7468 (t160) REVERT: A 182 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: A 224 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7146 (mm-30) REVERT: A 270 MET cc_start: 0.7793 (tpt) cc_final: 0.7422 (tpt) REVERT: A 305 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7766 (mm-40) REVERT: A 335 ASP cc_start: 0.7675 (t0) cc_final: 0.7471 (m-30) REVERT: A 416 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7016 (ptpt) REVERT: A 476 LYS cc_start: 0.7578 (tptt) cc_final: 0.7360 (tppt) REVERT: A 483 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: E 368 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7122 (mp) REVERT: E 450 ASN cc_start: 0.8526 (m-40) cc_final: 0.8225 (m110) REVERT: E 458 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7874 (mtmt) REVERT: E 471 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: H 4 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8026 (pp) REVERT: H 82 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: H 87 ARG cc_start: 0.7901 (mpt180) cc_final: 0.7614 (mtt180) REVERT: H 100 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7723 (tpp-160) REVERT: L 83 GLU cc_start: 0.8318 (pm20) cc_final: 0.8000 (pm20) REVERT: L 180 SER cc_start: 0.8257 (t) cc_final: 0.7949 (p) outliers start: 51 outliers final: 23 residues processed: 141 average time/residue: 0.6060 time to fit residues: 91.5570 Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 193 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 13 optimal weight: 0.0070 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.184242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143301 restraints weight = 9275.656| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.24 r_work: 0.3315 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9943 Z= 0.124 Angle : 0.562 8.053 13551 Z= 0.287 Chirality : 0.044 0.286 1470 Planarity : 0.004 0.042 1741 Dihedral : 4.510 35.430 1408 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.91 % Allowed : 22.14 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.97 (0.24), residues: 1216 helix: 1.73 (0.25), residues: 407 sheet: 0.90 (0.33), residues: 241 loop : -0.23 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 357 TYR 0.018 0.001 TYR A 385 PHE 0.014 0.001 PHE A 523 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9926) covalent geometry : angle 0.54982 / 0.28 (13517) SS BOND : bond 0.00810 / 0.64 ( 11) SS BOND : angle 1.78826 / 1.05 ( 22) hydrogen bonds : bond 0.04870 / 3.11 ( 427) hydrogen bonds : angle 4.77846 / 3.47 ( 1206) metal coordination : bond 0.00217 / 0.10 ( 2) link_NAG-ASN : bond 0.00567 / 0.27 ( 4) link_NAG-ASN : angle 3.25417 / 1.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: A 56 GLU cc_start: 0.6522 (mm-30) cc_final: 0.6059 (mm-30) REVERT: A 60 GLN cc_start: 0.8023 (mm110) cc_final: 0.7790 (mm-40) REVERT: A 102 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7209 (mm-40) REVERT: A 117 ASN cc_start: 0.7650 (t0) cc_final: 0.7401 (t160) REVERT: A 182 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6160 (mp0) REVERT: A 224 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7071 (mm-30) REVERT: A 299 ASP cc_start: 0.7669 (m-30) cc_final: 0.7468 (m-30) REVERT: A 305 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7709 (mm-40) REVERT: A 335 ASP cc_start: 0.7584 (t0) cc_final: 0.7360 (m-30) REVERT: A 416 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7072 (ptpt) REVERT: A 476 LYS cc_start: 0.7552 (tptt) cc_final: 0.7284 (tppt) REVERT: A 483 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: E 450 ASN cc_start: 0.8469 (m-40) cc_final: 0.8140 (m110) REVERT: E 458 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7838 (mtmt) REVERT: E 471 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: H 4 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7934 (pp) REVERT: H 82 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: H 87 ARG cc_start: 0.7835 (mpt180) cc_final: 0.7607 (mtt180) REVERT: H 89 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: H 100 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7586 (tpp-160) REVERT: L 83 GLU cc_start: 0.8230 (pm20) cc_final: 0.7979 (pm20) REVERT: L 180 SER cc_start: 0.8214 (t) cc_final: 0.7922 (p) outliers start: 41 outliers final: 17 residues processed: 138 average time/residue: 0.5839 time to fit residues: 86.5370 Evaluate side-chains 134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 193 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.181242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138616 restraints weight = 9280.123| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.31 r_work: 0.3261 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9943 Z= 0.171 Angle : 0.623 10.540 13551 Z= 0.318 Chirality : 0.046 0.303 1470 Planarity : 0.004 0.043 1741 Dihedral : 4.787 36.260 1408 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.91 % Allowed : 22.90 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.80 (0.24), residues: 1216 helix: 1.58 (0.25), residues: 407 sheet: 0.76 (0.32), residues: 252 loop : -0.31 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 357 TYR 0.018 0.002 TYR A 385 PHE 0.019 0.002 PHE A 523 TRP 0.011 0.001 TRP A 478 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 9926) covalent geometry : angle 0.61022 / 0.31 (13517) SS BOND : bond 0.00913 / 0.71 ( 11) SS BOND : angle 2.01591 / 1.14 ( 22) hydrogen bonds : bond 0.05573 / 3.55 ( 427) hydrogen bonds : angle 4.91741 / 3.58 ( 1206) metal coordination : bond 0.00464 / 0.22 ( 2) link_NAG-ASN : bond 0.00515 / 0.24 ( 4) link_NAG-ASN : angle 3.36592 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: A 56 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6141 (mm-30) REVERT: A 102 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7374 (mm-40) REVERT: A 117 ASN cc_start: 0.7642 (t0) cc_final: 0.7381 (t160) REVERT: A 179 LEU cc_start: 0.7602 (tt) cc_final: 0.7317 (pp) REVERT: A 182 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: A 224 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7132 (mm-30) REVERT: A 305 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7750 (mm-40) REVERT: A 416 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7005 (ptpt) REVERT: A 476 LYS cc_start: 0.7564 (tptt) cc_final: 0.7250 (tppt) REVERT: A 483 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: E 346 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7698 (mtp85) REVERT: E 368 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7095 (mp) REVERT: E 450 ASN cc_start: 0.8497 (m-40) cc_final: 0.8197 (m110) REVERT: E 458 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7890 (mtmt) REVERT: E 471 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8189 (mm-30) REVERT: H 4 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8055 (pp) REVERT: H 82 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: H 87 ARG cc_start: 0.7855 (mpt180) cc_final: 0.7579 (mtt180) REVERT: H 89 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: H 100 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7763 (tpp-160) REVERT: L 83 GLU cc_start: 0.8243 (pm20) cc_final: 0.8040 (pm20) REVERT: L 180 SER cc_start: 0.8410 (t) cc_final: 0.8100 (p) outliers start: 41 outliers final: 18 residues processed: 131 average time/residue: 0.5983 time to fit residues: 83.8714 Evaluate side-chains 134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 193 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.182216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141142 restraints weight = 9206.115| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.07 r_work: 0.3261 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9943 Z= 0.145 Angle : 0.592 10.953 13551 Z= 0.302 Chirality : 0.045 0.265 1470 Planarity : 0.004 0.043 1741 Dihedral : 4.678 36.122 1408 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.88 % Rotamer: Outliers : 3.24 % Allowed : 23.28 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.85 (0.24), residues: 1216 helix: 1.66 (0.25), residues: 407 sheet: 0.72 (0.32), residues: 251 loop : -0.27 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 357 TYR 0.018 0.001 TYR A 385 PHE 0.017 0.002 PHE A 523 TRP 0.011 0.001 TRP A 168 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9926) covalent geometry : angle 0.58138 / 0.30 (13517) SS BOND : bond 0.00859 / 0.66 ( 11) SS BOND : angle 1.53761 / 0.86 ( 22) hydrogen bonds : bond 0.05237 / 3.34 ( 427) hydrogen bonds : angle 4.86507 / 3.54 ( 1206) metal coordination : bond 0.00329 / 0.16 ( 2) link_NAG-ASN : bond 0.00602 / 0.29 ( 4) link_NAG-ASN : angle 3.24704 / 1.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: A 56 GLU cc_start: 0.6584 (mm-30) cc_final: 0.6144 (mm-30) REVERT: A 102 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7301 (mm-40) REVERT: A 117 ASN cc_start: 0.7674 (t0) cc_final: 0.7409 (t160) REVERT: A 179 LEU cc_start: 0.7576 (tt) cc_final: 0.7335 (pp) REVERT: A 182 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6150 (mp0) REVERT: A 224 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7138 (mm-30) REVERT: A 305 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7747 (mm-40) REVERT: A 416 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6994 (ptpt) REVERT: A 476 LYS cc_start: 0.7553 (tptt) cc_final: 0.7274 (tppt) REVERT: A 483 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: E 346 ARG cc_start: 0.8046 (ptm160) cc_final: 0.7766 (mtp85) REVERT: E 368 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7108 (mp) REVERT: E 450 ASN cc_start: 0.8494 (m-40) cc_final: 0.8186 (m110) REVERT: E 458 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7869 (mtmt) REVERT: E 471 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8190 (mm-30) REVERT: H 4 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7989 (pp) REVERT: H 82 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: H 87 ARG cc_start: 0.7875 (mpt180) cc_final: 0.7629 (mtt180) REVERT: H 100 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7693 (tpp-160) REVERT: L 180 SER cc_start: 0.8398 (t) cc_final: 0.8107 (p) outliers start: 34 outliers final: 18 residues processed: 132 average time/residue: 0.6237 time to fit residues: 88.1942 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 193 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.180423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138898 restraints weight = 9224.919| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.18 r_work: 0.3246 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9943 Z= 0.178 Angle : 0.633 11.497 13551 Z= 0.325 Chirality : 0.046 0.268 1470 Planarity : 0.004 0.044 1741 Dihedral : 4.907 36.924 1408 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 3.53 % Allowed : 23.00 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.74 (0.24), residues: 1216 helix: 1.51 (0.25), residues: 410 sheet: 0.73 (0.32), residues: 251 loop : -0.33 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 357 TYR 0.017 0.002 TYR A 385 PHE 0.019 0.002 PHE A 523 TRP 0.011 0.001 TRP A 478 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 9926) covalent geometry : angle 0.62204 / 0.32 (13517) SS BOND : bond 0.00908 / 0.70 ( 11) SS BOND : angle 1.80234 / 1.00 ( 22) hydrogen bonds : bond 0.05692 / 3.62 ( 427) hydrogen bonds : angle 4.98951 / 3.64 ( 1206) metal coordination : bond 0.00470 / 0.22 ( 2) link_NAG-ASN : bond 0.00659 / 0.31 ( 4) link_NAG-ASN : angle 3.34586 / 1.82 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: A 56 GLU cc_start: 0.6616 (mm-30) cc_final: 0.6163 (mm-30) REVERT: A 102 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7416 (mm-40) REVERT: A 117 ASN cc_start: 0.7690 (t0) cc_final: 0.7426 (t160) REVERT: A 182 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6052 (mp0) REVERT: A 224 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7147 (mm-30) REVERT: A 305 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7758 (mm-40) REVERT: A 341 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7424 (mmtm) REVERT: A 416 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.6984 (ptpt) REVERT: A 476 LYS cc_start: 0.7542 (tptt) cc_final: 0.7239 (tppt) REVERT: A 483 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: E 346 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7825 (mtp85) REVERT: E 368 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7123 (mp) REVERT: E 450 ASN cc_start: 0.8498 (m-40) cc_final: 0.8197 (m110) REVERT: E 458 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7892 (mtmt) REVERT: E 471 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: E 503 VAL cc_start: 0.8820 (t) cc_final: 0.8596 (m) REVERT: H 3 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7678 (mm-40) REVERT: H 4 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8027 (pp) REVERT: H 82 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: H 87 ARG cc_start: 0.7855 (mpt180) cc_final: 0.7592 (mtt180) REVERT: H 100 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7794 (tpp-160) REVERT: L 180 SER cc_start: 0.8423 (t) cc_final: 0.8195 (p) outliers start: 37 outliers final: 17 residues processed: 129 average time/residue: 0.6135 time to fit residues: 84.7391 Evaluate side-chains 130 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 193 HIS Chi-restraints excluded: chain L residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.181252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138863 restraints weight = 9182.542| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.38 r_work: 0.3290 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9943 Z= 0.151 Angle : 0.604 11.723 13551 Z= 0.308 Chirality : 0.045 0.245 1470 Planarity : 0.004 0.043 1741 Dihedral : 4.712 36.369 1408 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.21 % Favored : 96.71 % Rotamer: Outliers : 3.24 % Allowed : 23.28 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.78 (0.24), residues: 1216 helix: 1.56 (0.25), residues: 412 sheet: 0.72 (0.32), residues: 252 loop : -0.33 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 357 TYR 0.018 0.001 TYR A 385 PHE 0.017 0.002 PHE A 523 TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9926) covalent geometry : angle 0.59347 / 0.31 (13517) SS BOND : bond 0.00796 / 0.61 ( 11) SS BOND : angle 1.52752 / 0.85 ( 22) hydrogen bonds : bond 0.05307 / 3.38 ( 427) hydrogen bonds : angle 4.90769 / 3.58 ( 1206) metal coordination : bond 0.00333 / 0.16 ( 2) link_NAG-ASN : bond 0.00712 / 0.34 ( 4) link_NAG-ASN : angle 3.27284 / 1.77 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4365.30 seconds wall clock time: 75 minutes 11.41 seconds (4511.41 seconds total)