Starting phenix.real_space_refine on Fri Mar 15 00:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm1_13509/03_2024/7pm1_13509_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm1_13509/03_2024/7pm1_13509.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm1_13509/03_2024/7pm1_13509_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm1_13509/03_2024/7pm1_13509_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm1_13509/03_2024/7pm1_13509_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm1_13509/03_2024/7pm1_13509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm1_13509/03_2024/7pm1_13509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm1_13509/03_2024/7pm1_13509_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm1_13509/03_2024/7pm1_13509_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6482 2.51 5 N 1723 2.21 5 O 1897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 710": "NH1" <-> "NH2" Residue "A TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10169 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6130 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 27, 'TRANS': 723} Chain breaks: 3 Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2980 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="PHE C 375 "'] Classifications: {'peptide': 371, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351, None: 4} Not linked: pdbres="PHE C 375 " pdbres="ADP C 401 " Not linked: pdbres="ADP C 401 " pdbres="PO4 C 402 " Not linked: pdbres="PO4 C 402 " pdbres=" MG C 403 " Not linked: pdbres=" MG C 403 " pdbres="9UE C 404 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.92, per 1000 atoms: 0.58 Number of scatterers: 10169 At special positions: 0 Unit cell: (107.8, 130.9, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1897 8.00 N 1723 7.00 C 6482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 1.9 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 13 sheets defined 48.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.260A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.355A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.519A pdb=" N LEU A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 193 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 removed outlier: 3.532A pdb=" N VAL A 249 " --> pdb=" O LYS A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.611A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.768A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.695A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 removed outlier: 3.840A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.522A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 removed outlier: 3.712A pdb=" N ASN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 479 removed outlier: 3.545A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 493 through 499 removed outlier: 3.757A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 520 through 530 removed outlier: 4.216A pdb=" N ASN A 529 " --> pdb=" O GLN A 525 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.688A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 636 through 652 removed outlier: 3.569A pdb=" N HIS A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.758A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.875A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 724 through 735 removed outlier: 4.381A pdb=" N LYS A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.539A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.725A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.594A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.735A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.616A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.022A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.623A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.578A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.459A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.608A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 12 through 15 Processing sheet with id= C, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= D, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.543A pdb=" N LEU A 107 " --> pdb=" O TYR A 658 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 340 through 342 Processing sheet with id= F, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= G, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= H, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.722A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 removed outlier: 7.360A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 425 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2873 1.33 - 1.47: 2857 1.47 - 1.60: 4551 1.60 - 1.73: 3 1.73 - 1.87: 102 Bond restraints: 10386 Sorted by residual: bond pdb=" C4 9UE C 404 " pdb=" C5 9UE C 404 " ideal model delta sigma weight residual 0.880 1.501 -0.621 2.00e-02 2.50e+03 9.63e+02 bond pdb=" C11 9UE C 404 " pdb=" C12 9UE C 404 " ideal model delta sigma weight residual 2.064 1.522 0.542 2.00e-02 2.50e+03 7.34e+02 bond pdb=" C9 9UE C 404 " pdb=" N1 9UE C 404 " ideal model delta sigma weight residual 1.863 1.365 0.498 2.00e-02 2.50e+03 6.19e+02 bond pdb=" O 9UE C 404 " pdb=" C4 9UE C 404 " ideal model delta sigma weight residual 0.887 1.334 -0.447 2.00e-02 2.50e+03 5.00e+02 bond pdb=" C7 9UE C 404 " pdb=" C8 9UE C 404 " ideal model delta sigma weight residual 1.139 1.532 -0.393 2.00e-02 2.50e+03 3.87e+02 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.81: 236 105.81 - 113.68: 5719 113.68 - 121.55: 5807 121.55 - 129.42: 2198 129.42 - 137.29: 68 Bond angle restraints: 14028 Sorted by residual: angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " ideal model delta sigma weight residual 73.46 130.48 -57.02 3.00e+00 1.11e-01 3.61e+02 angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C22 9UE C 404 " ideal model delta sigma weight residual 176.54 124.04 52.50 3.00e+00 1.11e-01 3.06e+02 angle pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 78.92 130.29 -51.37 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C13 9UE C 404 " pdb=" C14 9UE C 404 " pdb=" C16 9UE C 404 " ideal model delta sigma weight residual 67.70 114.09 -46.39 3.00e+00 1.11e-01 2.39e+02 angle pdb=" N3 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 73.72 118.25 -44.53 3.00e+00 1.11e-01 2.20e+02 ... (remaining 14023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 6096 32.10 - 64.20: 117 64.20 - 96.30: 31 96.30 - 128.41: 7 128.41 - 160.51: 5 Dihedral angle restraints: 6256 sinusoidal: 2572 harmonic: 3684 Sorted by residual: dihedral pdb=" CD ARG A 92 " pdb=" NE ARG A 92 " pdb=" CZ ARG A 92 " pdb=" NH1 ARG A 92 " ideal model delta sinusoidal sigma weight residual 0.00 62.12 -62.12 1 1.00e+01 1.00e-02 5.11e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 159.19 140.80 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" CA GLY A 563 " pdb=" C GLY A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta harmonic sigma weight residual 180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 6253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1516 0.154 - 0.307: 10 0.307 - 0.461: 0 0.461 - 0.615: 1 0.615 - 0.769: 1 Chirality restraints: 1528 Sorted by residual: chirality pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C29 9UE C 404 " pdb=" C5 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -1.88 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C12 9UE C 404 " pdb=" C11 9UE C 404 " pdb=" C13 9UE C 404 " pdb=" C17 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.99 2.45 0.53 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" C1 9UE C 404 " pdb=" C 9UE C 404 " pdb=" C15 9UE C 404 " pdb=" C2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -2.39 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1525 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " 0.385 9.50e-02 1.11e+02 1.99e-01 1.42e+02 pdb=" NE ARG A 92 " -0.092 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " 0.188 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " -0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " 0.316 9.50e-02 1.11e+02 1.45e-01 2.49e+01 pdb=" NE ARG A 213 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.104 9.50e-02 1.11e+02 5.93e-02 1.83e+01 pdb=" NE ARG C 147 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.070 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.020 2.00e-02 2.50e+03 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 112 2.65 - 3.21: 9720 3.21 - 3.77: 15089 3.77 - 4.34: 21530 4.34 - 4.90: 34606 Nonbonded interactions: 81057 Sorted by model distance: nonbonded pdb=" O GLU A 71 " pdb=" NH2 ARG A 92 " model vdw 2.081 2.520 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.193 2.440 nonbonded pdb=" OE1 GLU B 118 " pdb=" NH1 ARG A 779 " model vdw 2.198 2.520 nonbonded pdb=" NH2 ARG B 37 " pdb=" O PRO B 43 " model vdw 2.220 2.520 nonbonded pdb=" OH TYR A 528 " pdb=" O ALA A 547 " model vdw 2.273 2.440 ... (remaining 81052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.020 Extract box with map and model: 6.980 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.600 Find NCS groups from input model: 0.260 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.014 0.621 10386 Z= 1.067 Angle : 1.400 57.019 14028 Z= 0.619 Chirality : 0.055 0.769 1528 Planarity : 0.010 0.199 1797 Dihedral : 16.226 160.508 3882 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.20), residues: 1242 helix: -1.79 (0.16), residues: 574 sheet: 0.22 (0.36), residues: 162 loop : -0.20 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP C 79 HIS 0.014 0.002 HIS A 418 PHE 0.042 0.002 PHE A 671 TYR 0.039 0.007 TYR C 306 ARG 0.193 0.013 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.9061 (m-10) cc_final: 0.8802 (m-10) REVERT: B 93 PHE cc_start: 0.9398 (m-80) cc_final: 0.9038 (m-80) REVERT: A 217 SER cc_start: 0.9092 (t) cc_final: 0.8486 (p) REVERT: A 239 MET cc_start: 0.7797 (mtp) cc_final: 0.7589 (ttm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2533 time to fit residues: 70.7504 Evaluate side-chains 102 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS A 88 ASN A 264 GLN A 398 ASN A 455 ASN A 463 GLN A 464 GLN A 638 HIS A 726 GLN A 775 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10386 Z= 0.192 Angle : 0.876 47.389 14028 Z= 0.388 Chirality : 0.044 0.262 1528 Planarity : 0.005 0.065 1797 Dihedral : 12.504 174.433 1400 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.75 % Allowed : 6.27 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1242 helix: 0.42 (0.20), residues: 592 sheet: 0.51 (0.35), residues: 177 loop : 0.49 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 79 HIS 0.011 0.002 HIS C 371 PHE 0.020 0.001 PHE B 144 TYR 0.013 0.001 TYR A 387 ARG 0.008 0.001 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9458 (m-80) cc_final: 0.8957 (m-80) REVERT: A 296 ILE cc_start: 0.9129 (tp) cc_final: 0.8701 (tt) REVERT: A 364 MET cc_start: 0.8327 (mmm) cc_final: 0.7946 (mmm) REVERT: C 123 MET cc_start: 0.8414 (mmm) cc_final: 0.8006 (mmm) REVERT: C 299 MET cc_start: 0.8966 (mmm) cc_final: 0.8763 (mmm) outliers start: 19 outliers final: 11 residues processed: 127 average time/residue: 0.2428 time to fit residues: 43.9899 Evaluate side-chains 98 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 113 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 101 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10386 Z= 0.188 Angle : 0.827 47.281 14028 Z= 0.355 Chirality : 0.042 0.228 1528 Planarity : 0.004 0.080 1797 Dihedral : 11.986 162.470 1400 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.94 % Allowed : 7.29 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1242 helix: 1.05 (0.21), residues: 591 sheet: 0.74 (0.37), residues: 171 loop : 0.72 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 484 HIS 0.008 0.001 HIS C 371 PHE 0.016 0.001 PHE B 96 TYR 0.014 0.001 TYR A 387 ARG 0.005 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.8904 (m-10) cc_final: 0.8669 (m-80) REVERT: B 93 PHE cc_start: 0.9492 (m-80) cc_final: 0.9012 (m-80) REVERT: A 296 ILE cc_start: 0.9131 (tp) cc_final: 0.8725 (tt) outliers start: 21 outliers final: 14 residues processed: 102 average time/residue: 0.2162 time to fit residues: 32.9946 Evaluate side-chains 98 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 0.0060 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 32 optimal weight: 0.0050 chunk 100 optimal weight: 2.9990 overall best weight: 0.7614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS A 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10386 Z= 0.206 Angle : 0.811 47.316 14028 Z= 0.344 Chirality : 0.042 0.226 1528 Planarity : 0.004 0.061 1797 Dihedral : 11.499 157.687 1400 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.94 % Allowed : 8.12 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1242 helix: 1.37 (0.22), residues: 583 sheet: 0.54 (0.38), residues: 178 loop : 0.65 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.007 0.001 HIS A 418 PHE 0.015 0.001 PHE C 255 TYR 0.012 0.001 TYR A 387 ARG 0.005 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8757 (tpp) cc_final: 0.8499 (tpp) REVERT: B 93 PHE cc_start: 0.9495 (m-80) cc_final: 0.9032 (m-80) REVERT: A 473 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8002 (mm-30) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.2126 time to fit residues: 34.3807 Evaluate side-chains 102 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 484 TRP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10386 Z= 0.306 Angle : 0.839 47.544 14028 Z= 0.361 Chirality : 0.043 0.264 1528 Planarity : 0.004 0.082 1797 Dihedral : 11.379 162.544 1400 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.75 % Allowed : 10.70 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1242 helix: 1.36 (0.22), residues: 583 sheet: 0.48 (0.38), residues: 180 loop : 0.50 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.006 0.001 HIS C 371 PHE 0.037 0.002 PHE B 12 TYR 0.021 0.001 TYR A 263 ARG 0.007 0.001 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9470 (m-80) cc_final: 0.8976 (m-80) REVERT: A 473 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8060 (mm-30) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 0.2037 time to fit residues: 30.2644 Evaluate side-chains 97 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 120 optimal weight: 0.0470 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10386 Z= 0.183 Angle : 0.793 47.434 14028 Z= 0.333 Chirality : 0.041 0.263 1528 Planarity : 0.004 0.084 1797 Dihedral : 11.170 165.371 1400 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.66 % Allowed : 11.53 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1242 helix: 1.52 (0.22), residues: 582 sheet: 0.54 (0.38), residues: 180 loop : 0.53 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.006 0.001 HIS C 275 PHE 0.054 0.001 PHE B 12 TYR 0.017 0.001 TYR A 263 ARG 0.008 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9465 (m-80) cc_final: 0.8991 (m-80) REVERT: A 473 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8088 (mm-30) outliers start: 18 outliers final: 14 residues processed: 98 average time/residue: 0.1999 time to fit residues: 29.7422 Evaluate side-chains 100 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10386 Z= 0.228 Angle : 0.791 47.499 14028 Z= 0.335 Chirality : 0.041 0.276 1528 Planarity : 0.004 0.074 1797 Dihedral : 11.122 167.346 1400 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.66 % Allowed : 12.08 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1242 helix: 1.60 (0.22), residues: 583 sheet: 0.40 (0.36), residues: 190 loop : 0.50 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.005 0.001 HIS C 275 PHE 0.050 0.001 PHE B 12 TYR 0.019 0.001 TYR A 263 ARG 0.009 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8761 (tpp) cc_final: 0.8429 (tpp) REVERT: B 93 PHE cc_start: 0.9451 (m-80) cc_final: 0.8973 (m-80) REVERT: A 418 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7347 (m90) REVERT: C 162 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.8044 (m-40) outliers start: 18 outliers final: 15 residues processed: 98 average time/residue: 0.2089 time to fit residues: 30.4719 Evaluate side-chains 101 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10386 Z= 0.242 Angle : 0.797 47.506 14028 Z= 0.339 Chirality : 0.042 0.277 1528 Planarity : 0.004 0.069 1797 Dihedral : 11.126 168.544 1400 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.75 % Allowed : 12.36 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1242 helix: 1.58 (0.22), residues: 588 sheet: 0.37 (0.37), residues: 190 loop : 0.48 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.005 0.001 HIS C 275 PHE 0.052 0.001 PHE B 12 TYR 0.018 0.001 TYR A 263 ARG 0.008 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8774 (tpp) cc_final: 0.8431 (tpp) REVERT: B 93 PHE cc_start: 0.9456 (m-80) cc_final: 0.8978 (m-80) REVERT: A 418 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7323 (m90) REVERT: C 162 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.8051 (m-40) outliers start: 19 outliers final: 14 residues processed: 101 average time/residue: 0.1935 time to fit residues: 29.3671 Evaluate side-chains 101 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 101 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10386 Z= 0.149 Angle : 0.786 47.440 14028 Z= 0.330 Chirality : 0.040 0.278 1528 Planarity : 0.004 0.069 1797 Dihedral : 10.962 169.884 1400 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.66 % Allowed : 12.82 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1242 helix: 1.66 (0.22), residues: 591 sheet: 0.47 (0.37), residues: 190 loop : 0.50 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.006 0.001 HIS C 275 PHE 0.050 0.001 PHE B 12 TYR 0.013 0.001 TYR A 263 ARG 0.009 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8684 (tpp) cc_final: 0.8342 (tpp) REVERT: B 66 ASP cc_start: 0.8872 (m-30) cc_final: 0.8004 (t70) REVERT: B 93 PHE cc_start: 0.9416 (m-80) cc_final: 0.8960 (m-80) REVERT: A 418 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7301 (m90) outliers start: 18 outliers final: 15 residues processed: 107 average time/residue: 0.1982 time to fit residues: 31.8778 Evaluate side-chains 104 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 0.0370 chunk 124 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 105 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10386 Z= 0.190 Angle : 0.796 47.437 14028 Z= 0.334 Chirality : 0.041 0.284 1528 Planarity : 0.004 0.058 1797 Dihedral : 10.973 171.053 1400 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.38 % Allowed : 13.28 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.56 (0.24), residues: 1242 helix: 1.71 (0.22), residues: 590 sheet: 0.50 (0.37), residues: 190 loop : 0.54 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS C 275 PHE 0.054 0.001 PHE B 12 TYR 0.014 0.001 TYR A 263 ARG 0.009 0.000 ARG B 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8647 (tpp) cc_final: 0.8335 (tpp) REVERT: B 66 ASP cc_start: 0.8880 (m-30) cc_final: 0.8001 (t70) REVERT: B 93 PHE cc_start: 0.9414 (m-80) cc_final: 0.8957 (m-80) REVERT: B 120 MET cc_start: 0.7750 (mpp) cc_final: 0.7111 (mpp) REVERT: B 123 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7930 (pp20) REVERT: A 418 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7360 (m90) outliers start: 15 outliers final: 14 residues processed: 101 average time/residue: 0.1945 time to fit residues: 29.6100 Evaluate side-chains 103 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 14 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 463 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.085730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062995 restraints weight = 28751.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065346 restraints weight = 14233.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066929 restraints weight = 9026.802| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10386 Z= 0.150 Angle : 0.789 47.399 14028 Z= 0.327 Chirality : 0.040 0.284 1528 Planarity : 0.004 0.057 1797 Dihedral : 10.864 172.486 1400 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.38 % Allowed : 13.47 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.62 (0.24), residues: 1242 helix: 1.76 (0.22), residues: 591 sheet: 0.54 (0.37), residues: 190 loop : 0.56 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS C 275 PHE 0.055 0.001 PHE B 12 TYR 0.015 0.001 TYR C 294 ARG 0.010 0.000 ARG B 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.55 seconds wall clock time: 37 minutes 44.13 seconds (2264.13 seconds total)