Starting phenix.real_space_refine on Tue Aug 6 00:23:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsj_38620/08_2024/8xsj_38620.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsj_38620/08_2024/8xsj_38620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsj_38620/08_2024/8xsj_38620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsj_38620/08_2024/8xsj_38620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsj_38620/08_2024/8xsj_38620.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xsj_38620/08_2024/8xsj_38620.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6345 atoms to isotropic. 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 49 5.16 5 C 6192 2.51 5 N 1616 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9740 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1554 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "H" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1583 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1621 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.10, per 1000 atoms: 0.93 Number of scatterers: 9740 At special positions: 0 Unit cell: (76.5, 83.3, 180.2, 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 49 16.00 O 1882 8.00 N 1616 7.00 C 6192 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 B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 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 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 103 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 546 " Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 906 " pdb="ZN ZN A 906 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 906 " - pdb=" NE2 HIS A 374 " 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 16 sheets defined 37.0% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.550A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 4.026A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.755A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.653A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' 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: 3.666A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.635A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) 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 220 through 232 removed outlier: 3.910A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.741A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.704A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.798A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.819A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.661A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.305A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.602A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.804A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.783A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.250A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.392A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.650A pdb=" N ASN H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.580A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.817A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 153 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.502A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.493A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.058A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.785A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.207A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.207A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 160 through 163 removed outlier: 4.127A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.773A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 129 through 139 removed outlier: 5.979A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 145 through 148 412 hydrogen bonds defined for protein. 1130 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: 2.65 Time building geometry restraints manager: 3.99 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: 3109 1.34 - 1.46: 2109 1.46 - 1.58: 4704 1.58 - 1.69: 1 1.69 - 1.81: 74 Bond restraints: 9997 Sorted by residual: bond pdb=" N LYS B 356 " pdb=" CA LYS B 356 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.24e-02 6.50e+03 5.92e+00 bond pdb=" CB PRO B 479 " pdb=" CG PRO B 479 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.32e+00 bond pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 1.462 1.488 -0.027 1.46e-02 4.69e+03 3.30e+00 bond pdb=" C ARG B 355 " pdb=" N LYS B 356 " ideal model delta sigma weight residual 1.331 1.353 -0.022 1.38e-02 5.25e+03 2.48e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 9992 not shown) Histogram of bond angle deviations from ideal: 97.67 - 104.95: 190 104.95 - 112.23: 4866 112.23 - 119.51: 3331 119.51 - 126.78: 5040 126.78 - 134.06: 166 Bond angle restraints: 13593 Sorted by residual: angle pdb=" C ASP H 54 " pdb=" N ALA H 55 " pdb=" CA ALA H 55 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C LYS B 462 " pdb=" CA LYS B 462 " pdb=" CB LYS B 462 " ideal model delta sigma weight residual 110.47 116.73 -6.26 1.77e+00 3.19e-01 1.25e+01 angle pdb=" CA GLU H 157 " pdb=" C GLU H 157 " pdb=" N PRO H 158 " ideal model delta sigma weight residual 117.68 120.14 -2.46 7.10e-01 1.98e+00 1.20e+01 angle pdb=" N LYS B 462 " pdb=" CA LYS B 462 " pdb=" C LYS B 462 " ideal model delta sigma weight residual 110.13 106.21 3.92 1.15e+00 7.56e-01 1.16e+01 angle pdb=" CA PRO B 479 " pdb=" N PRO B 479 " pdb=" CD PRO B 479 " ideal model delta sigma weight residual 112.00 107.30 4.70 1.40e+00 5.10e-01 1.13e+01 ... (remaining 13588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5455 17.64 - 35.28: 448 35.28 - 52.92: 89 52.92 - 70.56: 18 70.56 - 88.20: 10 Dihedral angle restraints: 6020 sinusoidal: 2475 harmonic: 3545 Sorted by residual: dihedral pdb=" CA LEU L 94 " pdb=" C LEU L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual -180.00 -126.04 -53.96 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA PHE H 155 " pdb=" C PHE H 155 " pdb=" N PRO H 156 " pdb=" CA PRO H 156 " ideal model delta harmonic sigma weight residual -180.00 -148.80 -31.20 0 5.00e+00 4.00e-02 3.89e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -126.03 40.03 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 6017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1081 0.044 - 0.089: 282 0.089 - 0.133: 104 0.133 - 0.177: 5 0.177 - 0.221: 2 Chirality restraints: 1474 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA PRO H 156 " pdb=" N PRO H 156 " pdb=" C PRO H 156 " pdb=" CB PRO H 156 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 1471 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 479 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 94 " -0.065 5.00e-02 4.00e+02 9.83e-02 1.55e+01 pdb=" N PRO L 95 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO A 258 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.047 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 63 2.58 - 3.16: 7683 3.16 - 3.74: 14387 3.74 - 4.32: 20363 4.32 - 4.90: 34694 Nonbonded interactions: 77190 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 906 " model vdw 2.001 2.230 nonbonded pdb=" NH1 ARG A 306 " pdb=" OE2 GLU A 310 " model vdw 2.183 3.120 nonbonded pdb=" OD1 ASP L 50 " pdb=" OH TYR L 91 " model vdw 2.186 3.040 nonbonded pdb=" NZ LYS A 31 " pdb=" OE2 GLU A 35 " model vdw 2.198 3.120 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.244 3.120 ... (remaining 77185 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 34.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 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 0.091 9997 Z= 0.216 Angle : 0.627 7.421 13593 Z= 0.341 Chirality : 0.045 0.221 1474 Planarity : 0.006 0.101 1751 Dihedral : 13.657 88.198 3719 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1206 helix: 0.73 (0.28), residues: 384 sheet: 1.09 (0.33), residues: 261 loop : -1.10 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 271 HIS 0.008 0.001 HIS A 401 PHE 0.020 0.001 PHE A 400 TYR 0.014 0.001 TYR A 385 ARG 0.007 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 186 LEU cc_start: 0.7861 (tp) cc_final: 0.7586 (tp) REVERT: A 249 MET cc_start: 0.8232 (mtm) cc_final: 0.8010 (mtm) REVERT: A 351 LEU cc_start: 0.8658 (mt) cc_final: 0.8356 (mp) REVERT: A 586 ASN cc_start: 0.7030 (m-40) cc_final: 0.6810 (m-40) REVERT: B 438 SER cc_start: 0.7960 (t) cc_final: 0.7720 (t) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.9607 time to fit residues: 202.0505 Evaluate side-chains 183 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 50 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 374 HIS A 401 HIS ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9997 Z= 0.208 Angle : 0.591 7.254 13593 Z= 0.306 Chirality : 0.044 0.226 1474 Planarity : 0.006 0.096 1751 Dihedral : 5.715 58.995 1488 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 1.33 % Allowed : 9.51 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1206 helix: 1.05 (0.28), residues: 374 sheet: 1.07 (0.33), residues: 260 loop : -1.09 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.004 0.001 HIS A 239 PHE 0.019 0.001 PHE A 400 TYR 0.016 0.002 TYR A 385 ARG 0.009 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 78 THR cc_start: 0.7794 (m) cc_final: 0.7503 (p) REVERT: A 98 GLN cc_start: 0.8006 (tt0) cc_final: 0.7761 (tt0) REVERT: A 186 LEU cc_start: 0.7963 (tp) cc_final: 0.7717 (tp) REVERT: A 202 TYR cc_start: 0.7355 (t80) cc_final: 0.6499 (t80) REVERT: A 351 LEU cc_start: 0.8657 (mt) cc_final: 0.8387 (mp) REVERT: A 376 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7930 (tpp) REVERT: A 408 MET cc_start: 0.7989 (mmt) cc_final: 0.7502 (mmt) REVERT: A 586 ASN cc_start: 0.6996 (m-40) cc_final: 0.6766 (m-40) REVERT: H 60 TYR cc_start: 0.7823 (m-80) cc_final: 0.7376 (m-80) REVERT: H 86 LEU cc_start: 0.8782 (mp) cc_final: 0.8573 (mp) REVERT: L 105 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6500 (mp0) outliers start: 14 outliers final: 7 residues processed: 187 average time/residue: 0.8955 time to fit residues: 183.9094 Evaluate side-chains 178 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.2980 chunk 33 optimal weight: 0.3980 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 401 HIS ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9997 Z= 0.205 Angle : 0.579 8.876 13593 Z= 0.299 Chirality : 0.044 0.215 1474 Planarity : 0.005 0.094 1751 Dihedral : 5.329 59.954 1484 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.23 % Favored : 95.60 % Rotamer: Outliers : 2.19 % Allowed : 9.89 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1206 helix: 1.04 (0.28), residues: 373 sheet: 1.06 (0.34), residues: 261 loop : -1.08 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.005 0.001 HIS A 374 PHE 0.019 0.001 PHE A 400 TYR 0.017 0.001 TYR A 385 ARG 0.007 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: A 78 THR cc_start: 0.7804 (m) cc_final: 0.7576 (p) REVERT: A 186 LEU cc_start: 0.7961 (tp) cc_final: 0.7731 (tp) REVERT: A 202 TYR cc_start: 0.7408 (t80) cc_final: 0.6558 (t80) REVERT: A 351 LEU cc_start: 0.8660 (mt) cc_final: 0.8398 (mp) REVERT: A 376 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7903 (tpp) REVERT: A 419 LYS cc_start: 0.6364 (mtpp) cc_final: 0.6114 (mttm) REVERT: A 479 GLU cc_start: 0.6841 (tt0) cc_final: 0.6547 (mt-10) REVERT: A 586 ASN cc_start: 0.6938 (m-40) cc_final: 0.6696 (m-40) REVERT: H 60 TYR cc_start: 0.7869 (m-80) cc_final: 0.7302 (m-80) REVERT: H 86 LEU cc_start: 0.8779 (mp) cc_final: 0.8549 (mp) REVERT: L 17 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.5849 (m-30) REVERT: L 175 LEU cc_start: 0.7099 (tt) cc_final: 0.6881 (tm) outliers start: 23 outliers final: 12 residues processed: 185 average time/residue: 0.9132 time to fit residues: 185.9955 Evaluate side-chains 185 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 92 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 374 HIS B 405 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9997 Z= 0.227 Angle : 0.584 6.831 13593 Z= 0.303 Chirality : 0.044 0.216 1474 Planarity : 0.005 0.095 1751 Dihedral : 5.254 59.057 1484 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.23 % Favored : 95.60 % Rotamer: Outliers : 2.57 % Allowed : 11.03 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1206 helix: 1.03 (0.28), residues: 374 sheet: 1.16 (0.35), residues: 250 loop : -1.07 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.005 0.001 HIS H 35 PHE 0.019 0.001 PHE A 400 TYR 0.018 0.002 TYR A 385 ARG 0.007 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 78 THR cc_start: 0.7806 (m) cc_final: 0.7593 (p) REVERT: A 186 LEU cc_start: 0.7975 (tp) cc_final: 0.7748 (tp) REVERT: A 202 TYR cc_start: 0.7441 (t80) cc_final: 0.6587 (t80) REVERT: A 270 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6303 (tpt) REVERT: A 351 LEU cc_start: 0.8673 (mt) cc_final: 0.8400 (mp) REVERT: A 376 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7934 (tpp) REVERT: A 479 GLU cc_start: 0.6828 (tt0) cc_final: 0.6588 (mt-10) REVERT: A 586 ASN cc_start: 0.6870 (m-40) cc_final: 0.6638 (m-40) REVERT: H 108 MET cc_start: 0.6913 (ttp) cc_final: 0.6671 (ttm) REVERT: L 17 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.5955 (m-30) REVERT: L 90 GLN cc_start: 0.8437 (pp30) cc_final: 0.8097 (pp30) outliers start: 27 outliers final: 15 residues processed: 185 average time/residue: 0.9065 time to fit residues: 184.1589 Evaluate side-chains 196 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 1 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 104 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 374 HIS B 405 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9997 Z= 0.190 Angle : 0.565 7.506 13593 Z= 0.293 Chirality : 0.043 0.208 1474 Planarity : 0.005 0.092 1751 Dihedral : 5.137 57.273 1484 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 2.57 % Allowed : 11.69 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1206 helix: 1.09 (0.28), residues: 374 sheet: 1.18 (0.35), residues: 250 loop : -1.04 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE A 400 TYR 0.016 0.001 TYR H 102 ARG 0.009 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: A 186 LEU cc_start: 0.7958 (tp) cc_final: 0.7744 (tp) REVERT: A 202 TYR cc_start: 0.7457 (t80) cc_final: 0.6622 (t80) REVERT: A 270 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6293 (tpt) REVERT: A 351 LEU cc_start: 0.8663 (mt) cc_final: 0.8410 (mp) REVERT: A 586 ASN cc_start: 0.6835 (m-40) cc_final: 0.6595 (m-40) REVERT: L 17 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.5999 (m-30) outliers start: 27 outliers final: 16 residues processed: 184 average time/residue: 0.8610 time to fit residues: 175.0258 Evaluate side-chains 188 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 405 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9997 Z= 0.259 Angle : 0.595 6.841 13593 Z= 0.309 Chirality : 0.044 0.213 1474 Planarity : 0.005 0.096 1751 Dihedral : 5.180 54.545 1484 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.35 % Rotamer: Outliers : 2.57 % Allowed : 12.45 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1206 helix: 0.96 (0.28), residues: 374 sheet: 1.15 (0.35), residues: 250 loop : -1.11 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.005 0.001 HIS H 35 PHE 0.018 0.001 PHE A 400 TYR 0.020 0.002 TYR A 385 ARG 0.005 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: A 186 LEU cc_start: 0.8003 (tp) cc_final: 0.7777 (tp) REVERT: A 202 TYR cc_start: 0.7480 (t80) cc_final: 0.6641 (t80) REVERT: A 351 LEU cc_start: 0.8703 (mt) cc_final: 0.8414 (mp) REVERT: A 419 LYS cc_start: 0.6333 (mtpp) cc_final: 0.6066 (mttm) REVERT: A 586 ASN cc_start: 0.6850 (m-40) cc_final: 0.6624 (m-40) REVERT: H 86 LEU cc_start: 0.8782 (mt) cc_final: 0.8552 (mp) REVERT: L 17 ASP cc_start: 0.6711 (OUTLIER) cc_final: 0.6019 (m-30) outliers start: 27 outliers final: 18 residues processed: 183 average time/residue: 0.8303 time to fit residues: 167.7966 Evaluate side-chains 194 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 0.0040 chunk 115 optimal weight: 0.0050 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9997 Z= 0.173 Angle : 0.559 6.957 13593 Z= 0.289 Chirality : 0.043 0.203 1474 Planarity : 0.005 0.092 1751 Dihedral : 4.943 53.171 1484 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 2.38 % Allowed : 13.21 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1206 helix: 1.10 (0.28), residues: 374 sheet: 1.12 (0.35), residues: 250 loop : -1.04 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS H 35 PHE 0.026 0.001 PHE A 504 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: A 202 TYR cc_start: 0.7474 (t80) cc_final: 0.6653 (t80) REVERT: A 306 ARG cc_start: 0.7691 (tpt90) cc_final: 0.7377 (tpt90) REVERT: A 351 LEU cc_start: 0.8674 (mt) cc_final: 0.8421 (mp) REVERT: A 369 PHE cc_start: 0.7820 (t80) cc_final: 0.7566 (t80) REVERT: A 586 ASN cc_start: 0.6817 (m-40) cc_final: 0.6579 (m-40) REVERT: H 86 LEU cc_start: 0.8774 (mt) cc_final: 0.8535 (mp) REVERT: L 17 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.5962 (m-30) outliers start: 25 outliers final: 15 residues processed: 188 average time/residue: 0.9179 time to fit residues: 189.9595 Evaluate side-chains 197 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9997 Z= 0.327 Angle : 0.633 7.697 13593 Z= 0.329 Chirality : 0.046 0.219 1474 Planarity : 0.006 0.098 1751 Dihedral : 5.084 55.705 1484 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.06 % Favored : 94.77 % Rotamer: Outliers : 2.76 % Allowed : 12.74 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1206 helix: 0.90 (0.27), residues: 374 sheet: 1.11 (0.35), residues: 250 loop : -1.17 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 353 HIS 0.008 0.002 HIS H 35 PHE 0.024 0.002 PHE A 504 TYR 0.023 0.002 TYR A 385 ARG 0.005 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6405 (mp0) REVERT: A 83 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: A 117 ASN cc_start: 0.7150 (t0) cc_final: 0.6931 (t0) REVERT: A 202 TYR cc_start: 0.7486 (t80) cc_final: 0.6647 (t80) REVERT: A 270 MET cc_start: 0.7305 (tpp) cc_final: 0.7044 (tpt) REVERT: A 351 LEU cc_start: 0.8719 (mt) cc_final: 0.8412 (mp) REVERT: A 383 MET cc_start: 0.7721 (mtp) cc_final: 0.7391 (mtp) REVERT: A 408 MET cc_start: 0.8087 (mmt) cc_final: 0.7572 (mmt) REVERT: A 457 GLU cc_start: 0.8147 (tp30) cc_final: 0.7944 (tp30) REVERT: A 586 ASN cc_start: 0.6870 (m-40) cc_final: 0.6650 (m-40) REVERT: H 86 LEU cc_start: 0.8780 (mt) cc_final: 0.8549 (mp) REVERT: L 17 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6166 (m-30) outliers start: 29 outliers final: 18 residues processed: 186 average time/residue: 0.9122 time to fit residues: 185.8206 Evaluate side-chains 192 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 64 optimal weight: 0.0770 chunk 46 optimal weight: 0.0980 chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9997 Z= 0.204 Angle : 0.585 6.869 13593 Z= 0.303 Chirality : 0.044 0.210 1474 Planarity : 0.005 0.093 1751 Dihedral : 4.857 53.997 1484 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.23 % Favored : 95.60 % Rotamer: Outliers : 1.81 % Allowed : 13.88 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1206 helix: 1.02 (0.28), residues: 374 sheet: 1.09 (0.34), residues: 252 loop : -1.12 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.005 0.001 HIS H 35 PHE 0.023 0.001 PHE A 504 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6469 (mp0) REVERT: A 83 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7066 (m-80) REVERT: A 202 TYR cc_start: 0.7472 (t80) cc_final: 0.6600 (t80) REVERT: A 270 MET cc_start: 0.7288 (tpp) cc_final: 0.7022 (tpt) REVERT: A 351 LEU cc_start: 0.8683 (mt) cc_final: 0.8427 (mp) REVERT: A 383 MET cc_start: 0.7683 (mtp) cc_final: 0.7341 (mtp) REVERT: A 408 MET cc_start: 0.8055 (mmt) cc_final: 0.7575 (mmt) REVERT: A 431 ASP cc_start: 0.7004 (p0) cc_final: 0.6719 (p0) REVERT: A 586 ASN cc_start: 0.6839 (m-40) cc_final: 0.6613 (m-40) REVERT: H 86 LEU cc_start: 0.8764 (mt) cc_final: 0.8538 (mp) REVERT: L 17 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.5985 (m-30) outliers start: 19 outliers final: 16 residues processed: 181 average time/residue: 0.9101 time to fit residues: 181.0472 Evaluate side-chains 198 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9997 Z= 0.228 Angle : 0.605 10.514 13593 Z= 0.313 Chirality : 0.044 0.209 1474 Planarity : 0.005 0.095 1751 Dihedral : 4.815 54.582 1484 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 1.71 % Allowed : 14.54 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1206 helix: 1.05 (0.28), residues: 374 sheet: 1.11 (0.35), residues: 250 loop : -1.15 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.007 0.001 HIS H 35 PHE 0.030 0.001 PHE H 68 TYR 0.018 0.002 TYR A 385 ARG 0.004 0.000 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6472 (mp0) REVERT: A 117 ASN cc_start: 0.7139 (t0) cc_final: 0.6934 (t0) REVERT: A 202 TYR cc_start: 0.7474 (t80) cc_final: 0.6615 (t80) REVERT: A 270 MET cc_start: 0.7321 (tpp) cc_final: 0.7001 (tpt) REVERT: A 351 LEU cc_start: 0.8697 (mt) cc_final: 0.8421 (mp) REVERT: A 369 PHE cc_start: 0.7908 (t80) cc_final: 0.7640 (t80) REVERT: A 383 MET cc_start: 0.7681 (mtp) cc_final: 0.7308 (mtp) REVERT: A 408 MET cc_start: 0.8058 (mmt) cc_final: 0.7575 (mmt) REVERT: A 431 ASP cc_start: 0.6982 (p0) cc_final: 0.6684 (p0) REVERT: A 586 ASN cc_start: 0.6840 (m-40) cc_final: 0.6618 (m-40) REVERT: H 86 LEU cc_start: 0.8763 (mt) cc_final: 0.8533 (mp) REVERT: L 17 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6093 (m-30) outliers start: 18 outliers final: 14 residues processed: 184 average time/residue: 0.8721 time to fit residues: 176.8819 Evaluate side-chains 197 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.0000 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 0.0470 chunk 97 optimal weight: 5.9990 chunk 12 optimal weight: 0.0470 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 overall best weight: 0.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.163166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.137832 restraints weight = 22418.114| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.88 r_work: 0.3747 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9997 Z= 0.151 Angle : 0.563 10.213 13593 Z= 0.291 Chirality : 0.043 0.195 1474 Planarity : 0.005 0.091 1751 Dihedral : 4.602 52.661 1484 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.73 % Favored : 96.10 % Rotamer: Outliers : 1.05 % Allowed : 15.49 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1206 helix: 1.20 (0.28), residues: 375 sheet: 1.15 (0.34), residues: 253 loop : -1.11 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 478 HIS 0.007 0.001 HIS H 35 PHE 0.023 0.001 PHE A 504 TYR 0.010 0.001 TYR H 80 ARG 0.005 0.000 ARG A 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.29 seconds wall clock time: 72 minutes 11.70 seconds (4331.70 seconds total)