Starting phenix.real_space_refine on Fri Sep 11 14:56:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xi1_66893/09_2026/9xi1_66893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xi1_66893/09_2026/9xi1_66893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xi1_66893/09_2026/9xi1_66893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xi1_66893/09_2026/9xi1_66893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xi1_66893/09_2026/9xi1_66893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xi1_66893/09_2026/9xi1_66893.map" } resolution = 2.58 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= 0.033 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 50 5.16 5 C 6149 2.51 5 N 1608 2.21 5 O 1868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 9676 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: 1645 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1641 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 222, 1641 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1671 Chain: "L" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1570 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: 1.92, per 1000 atoms: 0.20 Number of scatterers: 9676 At special positions: 0 Unit cell: (77.592, 143.472, 125.172, 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 50 16.00 O 1868 8.00 N 1608 7.00 C 6149 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 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 432.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 19 sheets defined 38.3% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.573A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.614A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.712A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 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 219 through 252 removed outlier: 3.724A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.652A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.587A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.704A 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 removed outlier: 3.561A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.753A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.824A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.689A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.507A 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: 3.542A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.208A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.988A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.690A 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: 4.126A pdb=" N ASP A 615 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 364 through 371 removed outlier: 3.506A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.561A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 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 Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.809A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.921A 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: 6.159A 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: 3.592A 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: 6.694A 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: 5.950A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.041A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR H 110 " --> pdb=" O SER H 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 131 through 135 removed outlier: 5.225A pdb=" N ALA H 148 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL H 195 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY H 150 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL H 193 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU H 152 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER H 191 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS H 154 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU H 189 " --> pdb=" O LYS H 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 131 through 135 removed outlier: 5.225A pdb=" N ALA H 148 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL H 195 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY H 150 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL H 193 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU H 152 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER H 191 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS H 154 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU H 189 " --> pdb=" O LYS H 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER H 188 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.844A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.743A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.743A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'L' and resid 121 through 123 removed outlier: 3.775A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 121 through 123 removed outlier: 3.775A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.666A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1181 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: 1.46 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2948 1.34 - 1.46: 2035 1.46 - 1.58: 4877 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 9938 Sorted by residual: bond pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 1.462 1.488 -0.026 8.50e-03 1.38e+04 9.57e+00 bond pdb=" N VAL L 149 " pdb=" CA VAL L 149 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.18e+00 bond pdb=" N TYR L 145 " pdb=" CA TYR L 145 " ideal model delta sigma weight residual 1.462 1.488 -0.026 9.50e-03 1.11e+04 7.76e+00 bond pdb=" N LEU A 142 " pdb=" CA LEU A 142 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.34e-02 5.57e+03 7.36e+00 bond pdb=" N ASP E 389 " pdb=" CA ASP E 389 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.08e-02 8.57e+03 7.14e+00 ... (remaining 9933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 13474 3.43 - 6.85: 44 6.85 - 10.28: 9 10.28 - 13.70: 1 13.70 - 17.13: 1 Bond angle restraints: 13529 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 122.70 105.57 17.13 1.30e+00 5.92e-01 1.74e+02 angle pdb=" N LEU A 278 " pdb=" CA LEU A 278 " pdb=" C LEU A 278 " ideal model delta sigma weight residual 113.17 107.82 5.35 1.26e+00 6.30e-01 1.80e+01 angle pdb=" CA GLN H 43 " pdb=" CB GLN H 43 " pdb=" CG GLN H 43 " ideal model delta sigma weight residual 114.10 122.04 -7.94 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CA MET A 557 " pdb=" CB MET A 557 " pdb=" CG MET A 557 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CA GLU H 89 " pdb=" CB GLU H 89 " pdb=" CG GLU H 89 " ideal model delta sigma weight residual 114.10 121.48 -7.38 2.00e+00 2.50e-01 1.36e+01 ... (remaining 13524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 5123 18.03 - 36.06: 613 36.06 - 54.09: 135 54.09 - 72.13: 54 72.13 - 90.16: 20 Dihedral angle restraints: 5945 sinusoidal: 2373 harmonic: 3572 Sorted by residual: dihedral pdb=" CA ALA E 372 " pdb=" C ALA E 372 " pdb=" N PRO E 373 " pdb=" CA PRO E 373 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA GLU H 89 " pdb=" C GLU H 89 " pdb=" N ASP H 90 " pdb=" CA ASP H 90 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PHE E 371 " pdb=" C PHE E 371 " pdb=" N ALA E 372 " pdb=" CA ALA E 372 " ideal model delta harmonic sigma weight residual 180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1234 0.062 - 0.124: 213 0.124 - 0.185: 18 0.185 - 0.247: 1 0.247 - 0.309: 1 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CB ILE H 52 " pdb=" CA ILE H 52 " pdb=" CG1 ILE H 52 " pdb=" CG2 ILE H 52 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 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 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LEU L 185 " pdb=" N LEU L 185 " pdb=" C LEU L 185 " pdb=" CB LEU L 185 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1464 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 112 " -0.082 2.00e-02 2.50e+03 1.49e-01 2.21e+02 pdb=" C GLY L 112 " 0.257 2.00e-02 2.50e+03 pdb=" O GLY L 112 " -0.095 2.00e-02 2.50e+03 pdb=" N GLN L 113 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 276 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C THR A 276 " -0.062 2.00e-02 2.50e+03 pdb=" O THR A 276 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN A 277 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 52 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO H 53 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 53 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 53 " 0.027 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 77 2.60 - 3.18: 7536 3.18 - 3.75: 15768 3.75 - 4.33: 22042 4.33 - 4.90: 36249 Nonbonded interactions: 81672 Sorted by model distance: nonbonded pdb=" O ARG A 393 " pdb=" OD1 ASN A 394 " model vdw 2.029 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.262 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.285 3.040 nonbonded pdb=" O SER H 77 " pdb=" OG SER H 77 " model vdw 2.320 3.040 nonbonded pdb=" O THR A 125 " pdb=" OG1 THR A 129 " model vdw 2.323 3.040 ... (remaining 81667 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=0.39 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: 7.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9955 Z= 0.193 Angle : 0.659 17.126 13565 Z= 0.375 Chirality : 0.047 0.309 1467 Planarity : 0.006 0.149 1745 Dihedral : 17.512 90.158 3625 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.14 % Allowed : 26.00 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.23), residues: 1218 helix: -0.07 (0.23), residues: 413 sheet: 0.60 (0.32), residues: 263 loop : -0.76 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.027 0.001 TYR A 202 PHE 0.015 0.002 PHE A 369 TRP 0.012 0.001 TRP H 114 HIS 0.010 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.19 ( 9938) covalent geometry : angle 0.65498 / 0.37 (13529) SS BOND : bond 0.00171 / 0.11 ( 11) SS BOND : angle 0.51303 / 0.31 ( 24) hydrogen bonds : bond 0.18788 / 11.54 ( 417) hydrogen bonds : angle 7.28090 / 5.32 ( 1181) metal coordination : bond 0.00122 / 0.06 ( 2) link_NAG-ASN : bond 0.00275 / 0.12 ( 4) link_NAG-ASN : angle 2.57931 / 1.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 THR cc_start: 0.8596 (p) cc_final: 0.8323 (t) REVERT: H 82 GLU cc_start: 0.8589 (tt0) cc_final: 0.8312 (tt0) REVERT: H 113 VAL cc_start: 0.8456 (p) cc_final: 0.8206 (m) outliers start: 12 outliers final: 7 residues processed: 141 average time/residue: 0.5327 time to fit residues: 80.5025 Evaluate side-chains 107 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 184 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 325 GLN A 531 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.175229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121703 restraints weight = 8989.087| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.80 r_work: 0.3191 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9955 Z= 0.195 Angle : 0.613 6.970 13565 Z= 0.318 Chirality : 0.047 0.213 1467 Planarity : 0.005 0.037 1745 Dihedral : 5.585 51.943 1418 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.12 % Allowed : 21.54 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.23), residues: 1218 helix: 0.65 (0.25), residues: 418 sheet: 0.78 (0.32), residues: 258 loop : -0.62 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.018 0.002 TYR A 50 PHE 0.020 0.002 PHE E 371 TRP 0.013 0.002 TRP H 47 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 ( 9938) covalent geometry : angle 0.60582 / 0.32 (13529) SS BOND : bond 0.00606 / 0.30 ( 11) SS BOND : angle 1.10791 / 0.69 ( 24) hydrogen bonds : bond 0.05387 / 3.56 ( 417) hydrogen bonds : angle 5.23019 / 3.83 ( 1181) metal coordination : bond 0.00241 / 0.12 ( 2) link_NAG-ASN : bond 0.00190 / 0.09 ( 4) link_NAG-ASN : angle 2.96958 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: A 589 GLU cc_start: 0.7512 (tp30) cc_final: 0.7251 (tp30) REVERT: E 357 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8197 (ttm-80) REVERT: L 16 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7679 (pt0) REVERT: L 82 VAL cc_start: 0.7997 (t) cc_final: 0.7733 (p) REVERT: L 154 LYS cc_start: 0.6029 (OUTLIER) cc_final: 0.5668 (pptt) REVERT: L 199 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.5975 (mt0) outliers start: 54 outliers final: 21 residues processed: 154 average time/residue: 0.5287 time to fit residues: 87.5353 Evaluate side-chains 132 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 0 optimal weight: 3.9990 chunk 77 optimal weight: 0.0010 chunk 105 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 531 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.177557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.124192 restraints weight = 9021.413| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.69 r_work: 0.3242 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9955 Z= 0.119 Angle : 0.513 5.918 13565 Z= 0.264 Chirality : 0.043 0.211 1467 Planarity : 0.004 0.038 1745 Dihedral : 4.867 57.110 1415 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.98 % Allowed : 22.20 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.42 (0.24), residues: 1218 helix: 1.01 (0.25), residues: 417 sheet: 0.75 (0.32), residues: 254 loop : -0.46 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 482 TYR 0.019 0.001 TYR A 50 PHE 0.012 0.001 PHE L 144 TRP 0.011 0.001 TRP H 47 HIS 0.012 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 9938) covalent geometry : angle 0.50806 / 0.26 (13529) SS BOND : bond 0.00361 / 0.19 ( 11) SS BOND : angle 0.72458 / 0.43 ( 24) hydrogen bonds : bond 0.04426 / 2.96 ( 417) hydrogen bonds : angle 4.81061 / 3.53 ( 1181) metal coordination : bond 0.00076 / 0.04 ( 2) link_NAG-ASN : bond 0.00139 / 0.06 ( 4) link_NAG-ASN : angle 2.22699 / 1.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6732 (mp) REVERT: A 249 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7013 (mmm) REVERT: A 491 VAL cc_start: 0.6305 (OUTLIER) cc_final: 0.6105 (m) REVERT: A 589 GLU cc_start: 0.7435 (tp30) cc_final: 0.7184 (tp30) REVERT: E 343 ASN cc_start: 0.7407 (p0) cc_final: 0.7134 (t0) REVERT: H 111 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.7858 (mtm) REVERT: L 16 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7598 (pt0) outliers start: 42 outliers final: 18 residues processed: 144 average time/residue: 0.5363 time to fit residues: 82.9041 Evaluate side-chains 126 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 199 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 14 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 531 GLN A 586 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.173026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120130 restraints weight = 8982.625| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.80 r_work: 0.3137 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9955 Z= 0.142 Angle : 0.544 6.292 13565 Z= 0.279 Chirality : 0.045 0.218 1467 Planarity : 0.004 0.035 1745 Dihedral : 4.783 59.105 1411 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.12 % Allowed : 21.63 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.42 (0.24), residues: 1218 helix: 1.04 (0.26), residues: 418 sheet: 0.73 (0.32), residues: 258 loop : -0.49 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 454 TYR 0.020 0.001 TYR A 50 PHE 0.013 0.001 PHE E 371 TRP 0.011 0.001 TRP H 47 HIS 0.011 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9938) covalent geometry : angle 0.53825 / 0.28 (13529) SS BOND : bond 0.00439 / 0.22 ( 11) SS BOND : angle 0.84272 / 0.51 ( 24) hydrogen bonds : bond 0.04685 / 3.13 ( 417) hydrogen bonds : angle 4.79008 / 3.53 ( 1181) metal coordination : bond 0.00130 / 0.06 ( 2) link_NAG-ASN : bond 0.00203 / 0.08 ( 4) link_NAG-ASN : angle 2.65084 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 0.373 Fit side-chains REVERT: A 37 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: A 176 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6598 (mp) REVERT: A 589 GLU cc_start: 0.7406 (tp30) cc_final: 0.7168 (tp30) REVERT: H 51 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8409 (tp) REVERT: H 111 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8000 (mtm) REVERT: L 16 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: L 107 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.7980 (tmtt) REVERT: L 154 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.5505 (pptt) REVERT: L 199 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.5979 (mt0) outliers start: 54 outliers final: 27 residues processed: 153 average time/residue: 0.5330 time to fit residues: 87.5543 Evaluate side-chains 142 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 531 GLN A 586 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.172456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.119005 restraints weight = 8956.884| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.89 r_work: 0.3114 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9955 Z= 0.152 Angle : 0.555 6.929 13565 Z= 0.284 Chirality : 0.045 0.213 1467 Planarity : 0.004 0.037 1745 Dihedral : 4.846 58.972 1411 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.65 % Allowed : 21.92 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.24), residues: 1218 helix: 1.03 (0.26), residues: 418 sheet: 0.71 (0.32), residues: 253 loop : -0.46 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 454 TYR 0.021 0.002 TYR A 50 PHE 0.013 0.002 PHE A 523 TRP 0.011 0.001 TRP H 47 HIS 0.010 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 9938) covalent geometry : angle 0.54747 / 0.28 (13529) SS BOND : bond 0.00478 / 0.24 ( 11) SS BOND : angle 0.88879 / 0.53 ( 24) hydrogen bonds : bond 0.04758 / 3.18 ( 417) hydrogen bonds : angle 4.78548 / 3.53 ( 1181) metal coordination : bond 0.00139 / 0.07 ( 2) link_NAG-ASN : bond 0.00223 / 0.10 ( 4) link_NAG-ASN : angle 2.92557 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: A 192 ARG cc_start: 0.7336 (mtt180) cc_final: 0.6502 (mtm-85) REVERT: A 589 GLU cc_start: 0.7403 (tp30) cc_final: 0.7152 (tp30) REVERT: H 51 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8407 (tp) REVERT: H 111 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.7997 (mtm) REVERT: L 16 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: L 107 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.7970 (tmtt) REVERT: L 154 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.4894 (pptt) outliers start: 49 outliers final: 27 residues processed: 151 average time/residue: 0.5262 time to fit residues: 85.4332 Evaluate side-chains 141 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 340 GLN A 531 GLN A 586 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.173417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120649 restraints weight = 8992.884| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.90 r_work: 0.3135 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9955 Z= 0.127 Angle : 0.527 6.570 13565 Z= 0.270 Chirality : 0.044 0.194 1467 Planarity : 0.004 0.037 1745 Dihedral : 4.722 58.859 1411 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.65 % Allowed : 22.11 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.48 (0.24), residues: 1218 helix: 1.11 (0.26), residues: 418 sheet: 0.71 (0.32), residues: 253 loop : -0.42 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 454 TYR 0.022 0.001 TYR A 50 PHE 0.011 0.001 PHE A 523 TRP 0.011 0.001 TRP H 47 HIS 0.010 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9938) covalent geometry : angle 0.52088 / 0.27 (13529) SS BOND : bond 0.00393 / 0.20 ( 11) SS BOND : angle 0.75839 / 0.45 ( 24) hydrogen bonds : bond 0.04436 / 2.98 ( 417) hydrogen bonds : angle 4.67742 / 3.45 ( 1181) metal coordination : bond 0.00117 / 0.06 ( 2) link_NAG-ASN : bond 0.00153 / 0.07 ( 4) link_NAG-ASN : angle 2.72553 / 1.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: A 176 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6507 (mp) REVERT: A 192 ARG cc_start: 0.7375 (mtt180) cc_final: 0.6546 (mtm-85) REVERT: A 586 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7961 (p0) REVERT: A 589 GLU cc_start: 0.7464 (tp30) cc_final: 0.7235 (tp30) REVERT: E 343 ASN cc_start: 0.7456 (p0) cc_final: 0.7184 (t0) REVERT: H 31 ASN cc_start: 0.7677 (p0) cc_final: 0.7421 (p0) REVERT: H 111 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7939 (mtm) REVERT: H 152 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6980 (tp) REVERT: L 16 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: L 107 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8014 (tmtt) REVERT: L 154 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5475 (pptt) REVERT: L 199 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.6000 (mt0) outliers start: 49 outliers final: 27 residues processed: 153 average time/residue: 0.5296 time to fit residues: 86.7822 Evaluate side-chains 149 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 531 GLN A 586 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.173488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121865 restraints weight = 8944.788| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.76 r_work: 0.3142 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9955 Z= 0.128 Angle : 0.534 6.612 13565 Z= 0.273 Chirality : 0.044 0.192 1467 Planarity : 0.004 0.036 1745 Dihedral : 4.707 58.771 1411 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.17 % Allowed : 22.49 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.24), residues: 1218 helix: 1.12 (0.26), residues: 418 sheet: 0.70 (0.32), residues: 253 loop : -0.39 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 454 TYR 0.023 0.001 TYR A 50 PHE 0.011 0.001 PHE A 523 TRP 0.011 0.001 TRP H 47 HIS 0.010 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9938) covalent geometry : angle 0.52699 / 0.27 (13529) SS BOND : bond 0.00388 / 0.20 ( 11) SS BOND : angle 0.74513 / 0.44 ( 24) hydrogen bonds : bond 0.04428 / 2.97 ( 417) hydrogen bonds : angle 4.66724 / 3.44 ( 1181) metal coordination : bond 0.00114 / 0.06 ( 2) link_NAG-ASN : bond 0.00133 / 0.06 ( 4) link_NAG-ASN : angle 2.78410 / 1.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: A 176 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6558 (mp) REVERT: A 192 ARG cc_start: 0.7391 (mtt180) cc_final: 0.6567 (mtm-85) REVERT: A 586 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8024 (p0) REVERT: A 589 GLU cc_start: 0.7457 (tp30) cc_final: 0.7241 (tp30) REVERT: E 343 ASN cc_start: 0.7466 (p0) cc_final: 0.7214 (t0) REVERT: H 31 ASN cc_start: 0.7671 (p0) cc_final: 0.7437 (p0) REVERT: H 111 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.7934 (mtm) REVERT: H 152 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7003 (tp) REVERT: L 16 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: L 154 LYS cc_start: 0.5914 (OUTLIER) cc_final: 0.4881 (pptt) outliers start: 44 outliers final: 30 residues processed: 146 average time/residue: 0.5136 time to fit residues: 80.4413 Evaluate side-chains 147 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 208 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 64 optimal weight: 0.0050 chunk 106 optimal weight: 3.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 531 GLN A 586 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.174248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.122565 restraints weight = 8946.305| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.77 r_work: 0.3166 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9955 Z= 0.118 Angle : 0.525 6.519 13565 Z= 0.268 Chirality : 0.044 0.191 1467 Planarity : 0.004 0.038 1745 Dihedral : 4.638 58.946 1411 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.46 % Allowed : 22.58 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.24), residues: 1218 helix: 1.20 (0.26), residues: 417 sheet: 0.70 (0.32), residues: 253 loop : -0.34 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 454 TYR 0.023 0.001 TYR A 50 PHE 0.010 0.001 PHE A 315 TRP 0.011 0.001 TRP H 47 HIS 0.010 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9938) covalent geometry : angle 0.51770 / 0.27 (13529) SS BOND : bond 0.00349 / 0.18 ( 11) SS BOND : angle 0.67329 / 0.40 ( 24) hydrogen bonds : bond 0.04273 / 2.88 ( 417) hydrogen bonds : angle 4.62082 / 3.41 ( 1181) metal coordination : bond 0.00086 / 0.04 ( 2) link_NAG-ASN : bond 0.00230 / 0.09 ( 4) link_NAG-ASN : angle 2.93183 / 1.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: A 176 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6505 (mp) REVERT: A 192 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6544 (mtm-85) REVERT: A 332 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7723 (ptp) REVERT: A 589 GLU cc_start: 0.7415 (tp30) cc_final: 0.7179 (tp30) REVERT: E 343 ASN cc_start: 0.7417 (p0) cc_final: 0.7186 (t0) REVERT: H 31 ASN cc_start: 0.7655 (p0) cc_final: 0.7426 (p0) REVERT: H 152 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6939 (tp) REVERT: L 16 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: L 154 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.4848 (pptt) outliers start: 47 outliers final: 29 residues processed: 151 average time/residue: 0.5393 time to fit residues: 87.1402 Evaluate side-chains 146 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 184 SER Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 208 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 107 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 95 optimal weight: 0.0770 chunk 78 optimal weight: 4.9990 chunk 42 optimal weight: 0.0980 chunk 115 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 55 optimal weight: 0.0170 chunk 27 optimal weight: 0.1980 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 442 GLN A 531 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.178255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.127797 restraints weight = 9057.595| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.82 r_work: 0.3270 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9955 Z= 0.092 Angle : 0.482 6.383 13565 Z= 0.246 Chirality : 0.042 0.192 1467 Planarity : 0.003 0.037 1745 Dihedral : 4.338 58.702 1411 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.75 % Allowed : 24.57 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.24), residues: 1218 helix: 1.59 (0.26), residues: 404 sheet: 0.80 (0.32), residues: 258 loop : -0.30 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.023 0.001 TYR A 50 PHE 0.017 0.001 PHE A 369 TRP 0.014 0.001 TRP A 168 HIS 0.010 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 ( 9938) covalent geometry : angle 0.47511 / 0.24 (13529) SS BOND : bond 0.00206 / 0.12 ( 11) SS BOND : angle 0.44803 / 0.26 ( 24) hydrogen bonds : bond 0.03604 / 2.44 ( 417) hydrogen bonds : angle 4.41072 / 3.26 ( 1181) metal coordination : bond 0.00068 / 0.03 ( 2) link_NAG-ASN : bond 0.00366 / 0.16 ( 4) link_NAG-ASN : angle 2.87186 / 1.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.453 Fit side-chains REVERT: A 37 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: A 176 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6497 (mp) REVERT: A 192 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6549 (mtm-85) REVERT: A 332 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7474 (ptp) REVERT: A 511 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.8043 (t) REVERT: L 16 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7881 (pt0) outliers start: 29 outliers final: 17 residues processed: 143 average time/residue: 0.5260 time to fit residues: 80.7358 Evaluate side-chains 135 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 531 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.173747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118737 restraints weight = 8965.166| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.79 r_work: 0.3151 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9955 Z= 0.135 Angle : 0.543 6.651 13565 Z= 0.277 Chirality : 0.045 0.207 1467 Planarity : 0.004 0.036 1745 Dihedral : 4.537 58.446 1410 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.66 % Allowed : 25.33 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.24), residues: 1218 helix: 1.31 (0.26), residues: 417 sheet: 0.67 (0.32), residues: 262 loop : -0.28 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.024 0.001 TYR A 50 PHE 0.013 0.001 PHE A 315 TRP 0.011 0.001 TRP A 168 HIS 0.010 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9938) covalent geometry : angle 0.53512 / 0.28 (13529) SS BOND : bond 0.00387 / 0.20 ( 11) SS BOND : angle 0.74608 / 0.44 ( 24) hydrogen bonds : bond 0.04429 / 2.97 ( 417) hydrogen bonds : angle 4.61681 / 3.41 ( 1181) metal coordination : bond 0.00130 / 0.06 ( 2) link_NAG-ASN : bond 0.00195 / 0.08 ( 4) link_NAG-ASN : angle 2.98318 / 1.83 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.300 Fit side-chains REVERT: A 37 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: A 176 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6468 (mp) REVERT: A 192 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6506 (mtm-85) REVERT: L 16 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: L 154 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.4832 (pptt) outliers start: 28 outliers final: 20 residues processed: 137 average time/residue: 0.5156 time to fit residues: 76.1373 Evaluate side-chains 134 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain L residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 531 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123866 restraints weight = 8961.033| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.52 r_work: 0.3168 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9955 Z= 0.139 Angle : 0.551 6.716 13565 Z= 0.283 Chirality : 0.045 0.252 1467 Planarity : 0.004 0.038 1745 Dihedral : 4.608 58.629 1410 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.96 % Favored : 96.96 % Rotamer: Outliers : 2.94 % Allowed : 24.86 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.24), residues: 1218 helix: 1.26 (0.26), residues: 417 sheet: 0.65 (0.32), residues: 262 loop : -0.31 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 454 TYR 0.026 0.001 TYR A 50 PHE 0.013 0.001 PHE A 315 TRP 0.011 0.001 TRP A 168 HIS 0.010 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9938) covalent geometry : angle 0.54455 / 0.28 (13529) SS BOND : bond 0.00411 / 0.21 ( 11) SS BOND : angle 0.77985 / 0.46 ( 24) hydrogen bonds : bond 0.04512 / 3.02 ( 417) hydrogen bonds : angle 4.67548 / 3.45 ( 1181) metal coordination : bond 0.00130 / 0.06 ( 2) link_NAG-ASN : bond 0.00217 / 0.09 ( 4) link_NAG-ASN : angle 2.79203 / 1.70 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4165.20 seconds wall clock time: 71 minutes 34.32 seconds (4294.32 seconds total)