Starting phenix.real_space_refine (version: dev) on Sun Feb 19 12:34:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmj_13536/02_2023/7pmj_13536_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmj_13536/02_2023/7pmj_13536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmj_13536/02_2023/7pmj_13536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmj_13536/02_2023/7pmj_13536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmj_13536/02_2023/7pmj_13536_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmj_13536/02_2023/7pmj_13536_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "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 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 704": "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 ARG 724": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10085 Number of models: 1 Model: "" Number of chains: 6 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: 6001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 6001 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 27, 'TRANS': 706} Chain breaks: 6 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.97, per 1000 atoms: 0.59 Number of scatterers: 10085 At special positions: 0 Unit cell: (102.3, 138.6, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 5 15.00 Mg 3 11.99 O 1880 8.00 N 1713 7.00 C 6421 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: 4.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2356 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 13 sheets defined 49.4% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.163A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.644A 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: 4.686A 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 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 169 through 184 removed outlier: 3.762A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.770A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 270 removed outlier: 5.044A pdb=" N ALA A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.639A 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: 3.808A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.655A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.909A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 479 removed outlier: 3.505A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 476 " --> pdb=" O LEU A 472 " (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 500 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.797A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 568 removed outlier: 3.539A pdb=" N PHE A 564 " --> pdb=" O CYS A 561 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU A 565 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN A 568 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.973A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 652 removed outlier: 3.509A pdb=" N HIS A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.715A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.799A pdb=" N ARG A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 714 removed outlier: 3.750A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 735 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 removed outlier: 3.622A pdb=" N TRP A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) 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 80 through 92 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.562A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.601A 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 183 through 196 removed outlier: 3.588A pdb=" N ASP C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 262 Proline residue: C 258 - end of helix removed outlier: 4.811A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 removed outlier: 4.011A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.728A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.175A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.671A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 103 through 105 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 40 Processing sheet with id= D, first strand: chain 'A' and resid 100 through 103 Processing sheet with id= E, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.602A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 377 through 381 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: 3.599A 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 11 removed outlier: 3.514A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 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: 6.407A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.527A 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 241 431 hydrogen bonds defined for protein. 1209 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: 3.24 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1701 1.32 - 1.45: 2743 1.45 - 1.57: 5744 1.57 - 1.70: 9 1.70 - 1.83: 102 Bond restraints: 10299 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.444 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.584 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.453 0.072 2.10e-02 2.27e+03 1.16e+01 ... (remaining 10294 not shown) Histogram of bond angle deviations from ideal: 97.36 - 106.21: 286 106.21 - 115.07: 6174 115.07 - 123.93: 7203 123.93 - 132.78: 236 132.78 - 141.64: 16 Bond angle restraints: 13915 Sorted by residual: angle pdb=" CB MET A 783 " pdb=" CG MET A 783 " pdb=" SD MET A 783 " ideal model delta sigma weight residual 112.70 141.64 -28.94 3.00e+00 1.11e-01 9.30e+01 angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 108.92 18.03 3.00e+00 1.11e-01 3.61e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 110.92 10.78 1.80e+00 3.09e-01 3.58e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 101.59 8.51 1.90e+00 2.77e-01 2.01e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.03 4.37 1.00e+00 1.00e+00 1.91e+01 ... (remaining 13910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.62: 5944 26.62 - 53.24: 183 53.24 - 79.86: 41 79.86 - 106.48: 14 106.48 - 133.10: 3 Dihedral angle restraints: 6185 sinusoidal: 2532 harmonic: 3653 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.90 133.10 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" CA ALA A 554 " pdb=" C ALA A 554 " pdb=" N ASP A 555 " pdb=" CA ASP A 555 " ideal model delta harmonic sigma weight residual 180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 57.12 -117.12 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 6182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1070 0.061 - 0.121: 368 0.121 - 0.182: 73 0.182 - 0.243: 5 0.243 - 0.303: 3 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CA GLU C 316 " pdb=" N GLU C 316 " pdb=" C GLU C 316 " pdb=" CB GLU C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU A 782 " pdb=" CB LEU A 782 " pdb=" CD1 LEU A 782 " pdb=" CD2 LEU A 782 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1516 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.002 2.00e-02 2.50e+03 4.21e-02 3.54e+01 pdb=" CG TYR C 306 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.061 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 784 " 0.108 9.50e-02 1.11e+02 6.58e-02 2.61e+01 pdb=" NE ARG A 784 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 784 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG A 784 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 784 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 711 " 0.008 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR A 711 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 711 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 711 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 711 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 711 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR A 711 " -0.044 2.00e-02 2.50e+03 pdb=" OH TYR A 711 " 0.042 2.00e-02 2.50e+03 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 4 2.03 - 2.75: 1327 2.75 - 3.46: 14414 3.46 - 4.18: 23547 4.18 - 4.90: 42115 Nonbonded interactions: 81407 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.310 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.729 3.620 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.867 2.170 nonbonded pdb=" O1A ANP A1901 " pdb="MG MG A1903 " model vdw 1.947 2.170 nonbonded pdb=" O1B ANP A1901 " pdb="MG MG A1902 " model vdw 2.042 2.170 ... (remaining 81402 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6421 2.51 5 N 1713 2.21 5 O 1880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 7.980 Check model and map are aligned: 0.140 Process input model: 28.820 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.010 0.151 10299 Z= 0.648 Angle : 1.115 28.938 13915 Z= 0.623 Chirality : 0.061 0.303 1519 Planarity : 0.008 0.066 1773 Dihedral : 15.319 133.101 3829 Min Nonbonded Distance : 1.310 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.17 % 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: -1.97 (0.20), residues: 1220 helix: -1.98 (0.16), residues: 613 sheet: -0.23 (0.38), residues: 160 loop : -0.33 (0.26), residues: 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.239 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: symmetry clash outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.3247 time to fit residues: 40.5063 Evaluate side-chains 56 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 1.282 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2420 time to fit residues: 2.0457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN B 75 GLN A 81 HIS A 130 GLN A 264 GLN A 283 ASN A 354 HIS A 463 GLN A 642 ASN A 726 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 296 ASN C 371 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 10299 Z= 0.191 Angle : 0.631 7.918 13915 Z= 0.330 Chirality : 0.042 0.197 1519 Planarity : 0.004 0.044 1773 Dihedral : 8.526 117.869 1377 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.08 % 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: 0.52 (0.23), residues: 1220 helix: 0.33 (0.20), residues: 617 sheet: 0.80 (0.40), residues: 157 loop : 0.49 (0.29), residues: 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 1.271 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 outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 0.2634 time to fit residues: 24.5293 Evaluate side-chains 54 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1145 time to fit residues: 2.1185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 HIS B 147 HIS A 410 ASN A 455 ASN A 466 ASN C 161 HIS C 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 10299 Z= 0.149 Angle : 0.543 7.862 13915 Z= 0.279 Chirality : 0.040 0.157 1519 Planarity : 0.004 0.049 1773 Dihedral : 7.513 120.381 1377 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.08 % 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: 1.24 (0.24), residues: 1220 helix: 1.06 (0.21), residues: 619 sheet: 0.99 (0.42), residues: 151 loop : 0.65 (0.29), residues: 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 1.265 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 outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 0.2811 time to fit residues: 23.9333 Evaluate side-chains 53 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0892 time to fit residues: 1.9872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 0.0000 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 0.0570 overall best weight: 0.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 10299 Z= 0.140 Angle : 0.521 8.484 13915 Z= 0.261 Chirality : 0.039 0.167 1519 Planarity : 0.003 0.039 1773 Dihedral : 6.970 111.366 1377 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.08 % 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: 1.60 (0.24), residues: 1220 helix: 1.47 (0.22), residues: 612 sheet: 1.04 (0.41), residues: 158 loop : 0.70 (0.30), residues: 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.3124 time to fit residues: 24.9899 Evaluate side-chains 48 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1131 time to fit residues: 2.0889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 10299 Z= 0.165 Angle : 0.526 8.633 13915 Z= 0.263 Chirality : 0.040 0.168 1519 Planarity : 0.003 0.042 1773 Dihedral : 6.760 113.665 1377 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.08 % 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: 1.65 (0.24), residues: 1220 helix: 1.58 (0.22), residues: 617 sheet: 1.04 (0.41), residues: 164 loop : 0.59 (0.30), residues: 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 54 average time/residue: 0.2242 time to fit residues: 19.0513 Evaluate side-chains 45 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0917 time to fit residues: 1.9418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 568 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10299 Z= 0.137 Angle : 0.524 9.554 13915 Z= 0.258 Chirality : 0.039 0.171 1519 Planarity : 0.003 0.038 1773 Dihedral : 6.509 114.765 1377 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.08 % 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: 1.70 (0.25), residues: 1220 helix: 1.62 (0.22), residues: 617 sheet: 1.09 (0.41), residues: 164 loop : 0.59 (0.30), residues: 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.2090 time to fit residues: 18.1054 Evaluate side-chains 48 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1270 time to fit residues: 1.9276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 568 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10299 Z= 0.290 Angle : 0.581 9.558 13915 Z= 0.289 Chirality : 0.041 0.172 1519 Planarity : 0.003 0.039 1773 Dihedral : 6.756 124.045 1377 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % 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: 1.58 (0.24), residues: 1220 helix: 1.54 (0.21), residues: 622 sheet: 1.03 (0.39), residues: 168 loop : 0.50 (0.31), residues: 430 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2396 time to fit residues: 17.2795 Evaluate side-chains 46 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.0010 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.0000 chunk 113 optimal weight: 0.6980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 10299 Z= 0.128 Angle : 0.520 9.932 13915 Z= 0.254 Chirality : 0.039 0.174 1519 Planarity : 0.003 0.037 1773 Dihedral : 6.414 124.056 1377 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.08 % 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: 1.72 (0.25), residues: 1220 helix: 1.69 (0.22), residues: 616 sheet: 1.03 (0.41), residues: 162 loop : 0.54 (0.30), residues: 442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.2312 time to fit residues: 17.9406 Evaluate side-chains 48 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1005 time to fit residues: 1.9153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN A 568 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.004 0.028 10299 Z= 0.262 Angle : 0.581 11.812 13915 Z= 0.285 Chirality : 0.041 0.182 1519 Planarity : 0.003 0.037 1773 Dihedral : 6.586 128.966 1377 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.08 % 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: 1.62 (0.25), residues: 1220 helix: 1.59 (0.22), residues: 622 sheet: 1.12 (0.39), residues: 163 loop : 0.45 (0.31), residues: 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.2353 time to fit residues: 17.5031 Evaluate side-chains 47 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1100 time to fit residues: 1.8743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 97 optimal weight: 0.7980 chunk 10 optimal weight: 0.0270 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 10299 Z= 0.136 Angle : 0.567 13.036 13915 Z= 0.271 Chirality : 0.040 0.309 1519 Planarity : 0.003 0.037 1773 Dihedral : 6.313 123.625 1377 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.08 % 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: 1.74 (0.25), residues: 1220 helix: 1.65 (0.22), residues: 621 sheet: 1.22 (0.39), residues: 165 loop : 0.57 (0.31), residues: 434 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 1.410 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.2278 time to fit residues: 17.2205 Evaluate side-chains 47 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1790 time to fit residues: 2.2528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.0050 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.4252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.055859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.039518 restraints weight = 58739.082| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.50 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 10299 Z= 0.125 Angle : 0.534 10.622 13915 Z= 0.259 Chirality : 0.040 0.314 1519 Planarity : 0.003 0.037 1773 Dihedral : 6.070 119.081 1377 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % 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: 1.76 (0.25), residues: 1220 helix: 1.69 (0.22), residues: 622 sheet: 1.18 (0.41), residues: 157 loop : 0.57 (0.31), residues: 441 =============================================================================== Job complete usr+sys time: 1881.35 seconds wall clock time: 35 minutes 44.46 seconds (2144.46 seconds total)