Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 03:41:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmb_13527/10_2023/7pmb_13527_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmb_13527/10_2023/7pmb_13527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmb_13527/10_2023/7pmb_13527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmb_13527/10_2023/7pmb_13527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmb_13527/10_2023/7pmb_13527_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmb_13527/10_2023/7pmb_13527_updated.pdb" } resolution = 3.6 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6441 2.51 5 N 1719 2.21 5 O 1884 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 ARG 12": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A GLU 164": "OE1" <-> "OE2" 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 ARG 233": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A TYR 368": "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 TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 491": "OD1" <-> "OD2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 10113 Number of models: 1 Model: "" Number of chains: 6 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: "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: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 6043 Classifications: {'peptide': 739} Link IDs: {'PTRANS': 27, 'TRANS': 711} Chain breaks: 6 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "A" 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} 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: 6.66, per 1000 atoms: 0.66 Number of scatterers: 10113 At special positions: 0 Unit cell: (107.06, 136.74, 150.52, 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 4 15.00 Mg 2 11.99 O 1884 8.00 N 1719 7.00 C 6441 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: 5.18 Conformation dependent library (CDL) restraints added in 1.5 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 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: 2364 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 13 sheets defined 49.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.175A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.705A 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: 4.388A 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: 3.543A 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 127 Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.720A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.954A 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 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.533A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.588A pdb=" N THR A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 277' 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: 3.886A pdb=" N MET A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.590A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.700A pdb=" N PHE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.965A 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: 3.590A pdb=" N ILE A 454 " --> pdb=" O GLU A 450 " (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: 3.522A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.591A pdb=" N CYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.625A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 removed outlier: 5.036A pdb=" N LEU A 565 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 588 through 593 removed outlier: 3.920A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 636 through 651 Processing helix chain 'A' and resid 675 through 684 removed outlier: 4.056A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 725 through 735 removed outlier: 4.145A pdb=" N ASN A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 4.351A 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 753 through 791 removed outlier: 3.641A pdb=" N VAL A 756 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 765 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP A 781 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 791 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.677A pdb=" N GLN C 59 " --> pdb=" O ASP C 56 " (cutoff:3.500A) 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 125 removed outlier: 3.545A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.860A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.659A 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: 3.885A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.846A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.792A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.235A 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 284 Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.496A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.522A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.426A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 374 removed outlier: 4.208A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N CYS C 374 " --> pdb=" O HIS C 371 " (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 16 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 101 through 103 removed outlier: 3.561A pdb=" N LEU A 107 " --> pdb=" O TYR A 658 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 158 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 4.149A 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: 3.888A 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 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: 6.464A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.310A 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 241 427 hydrogen bonds defined for protein. 1104 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: 3.22 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1687 1.32 - 1.44: 2732 1.44 - 1.57: 5801 1.57 - 1.69: 6 1.69 - 1.81: 102 Bond restraints: 10328 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.202 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.60e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.40e-02 5.10e+03 8.33e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.33e+00 ... (remaining 10323 not shown) Histogram of bond angle deviations from ideal: 98.48 - 106.01: 255 106.01 - 113.54: 5679 113.54 - 121.07: 5295 121.07 - 128.60: 2650 128.60 - 136.13: 72 Bond angle restraints: 13951 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.81 11.89 1.80e+00 3.09e-01 4.37e+01 angle pdb=" CA TRP C 356 " pdb=" CB TRP C 356 " pdb=" CG TRP C 356 " ideal model delta sigma weight residual 113.60 122.80 -9.20 1.90e+00 2.77e-01 2.34e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.81 -4.81 1.10e+00 8.26e-01 1.91e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.06 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.21 4.19 1.00e+00 1.00e+00 1.75e+01 ... (remaining 13946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.17: 5972 27.17 - 54.34: 190 54.34 - 81.51: 41 81.51 - 108.69: 8 108.69 - 135.86: 4 Dihedral angle restraints: 6215 sinusoidal: 2550 harmonic: 3665 Sorted by residual: 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 75.86 -135.86 1 2.00e+01 2.50e-03 4.12e+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 -60.00 71.60 -131.60 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 67.63 -127.64 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 6212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1165 0.059 - 0.118: 287 0.118 - 0.177: 61 0.177 - 0.236: 9 0.236 - 0.295: 2 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CA TYR A 711 " pdb=" N TYR A 711 " pdb=" C TYR A 711 " pdb=" CB TYR A 711 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA HIS A 418 " pdb=" N HIS A 418 " pdb=" C HIS A 418 " pdb=" CB HIS A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG A 213 " pdb=" N ARG A 213 " pdb=" C ARG A 213 " pdb=" CB ARG A 213 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1521 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 28 " 0.133 9.50e-02 1.11e+02 7.79e-02 3.35e+01 pdb=" NE ARG C 28 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG C 28 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG C 28 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG C 28 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.140 9.50e-02 1.11e+02 7.83e-02 3.01e+01 pdb=" NE ARG A 677 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 477 " -0.001 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 477 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 477 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 477 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 477 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 477 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 477 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 477 " 0.050 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 4 2.03 - 2.75: 1262 2.75 - 3.47: 14606 3.47 - 4.18: 23313 4.18 - 4.90: 41709 Nonbonded interactions: 80894 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.317 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 1.947 2.170 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.021 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.136 2.170 ... (remaining 80889 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.990 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 32.820 Find NCS groups from input model: 0.270 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: 0.000 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: 44.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.006 0.122 10328 Z= 0.381 Angle : 0.933 11.894 13951 Z= 0.543 Chirality : 0.056 0.295 1524 Planarity : 0.009 0.117 1778 Dihedral : 15.724 135.857 3851 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % 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: -1.25 (0.21), residues: 1224 helix: -1.69 (0.17), residues: 566 sheet: 0.17 (0.36), residues: 155 loop : 0.23 (0.27), residues: 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.2652 time to fit residues: 50.5948 Evaluate side-chains 80 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.224 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0877 time to fit residues: 1.7988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.0470 chunk 37 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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** B 75 GLN A 264 GLN A 290 GLN A 354 HIS A 373 HIS A 398 ASN ** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 657 HIS A 755 GLN C 121 GLN C 161 HIS C 162 ASN C 173 HIS C 371 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10328 Z= 0.194 Angle : 0.661 10.028 13951 Z= 0.343 Chirality : 0.044 0.198 1524 Planarity : 0.005 0.047 1778 Dihedral : 9.939 136.769 1388 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.02 % Allowed : 5.85 % Favored : 93.13 % 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: 0.62 (0.23), residues: 1224 helix: 0.31 (0.20), residues: 574 sheet: 0.81 (0.37), residues: 163 loop : 0.69 (0.29), residues: 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 101 average time/residue: 0.2193 time to fit residues: 32.4396 Evaluate side-chains 77 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1059 time to fit residues: 2.3883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.8221 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10328 Z= 0.185 Angle : 0.600 8.149 13951 Z= 0.304 Chirality : 0.042 0.198 1524 Planarity : 0.004 0.050 1778 Dihedral : 8.493 134.346 1388 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.46 % Allowed : 8.64 % Favored : 90.90 % 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: 1.19 (0.24), residues: 1224 helix: 0.95 (0.22), residues: 585 sheet: 1.07 (0.39), residues: 160 loop : 0.72 (0.30), residues: 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 90 average time/residue: 0.2125 time to fit residues: 28.7312 Evaluate side-chains 71 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0970 time to fit residues: 2.0811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 462 GLN A 525 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10328 Z= 0.247 Angle : 0.598 8.476 13951 Z= 0.301 Chirality : 0.042 0.173 1524 Planarity : 0.004 0.041 1778 Dihedral : 8.039 138.338 1388 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.02 % Allowed : 10.58 % Favored : 88.39 % 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: 1.17 (0.24), residues: 1224 helix: 0.98 (0.22), residues: 592 sheet: 1.09 (0.39), residues: 154 loop : 0.63 (0.30), residues: 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 83 average time/residue: 0.2118 time to fit residues: 26.5120 Evaluate side-chains 70 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0951 time to fit residues: 2.2543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 0.035 10328 Z= 0.195 Angle : 0.582 9.349 13951 Z= 0.289 Chirality : 0.041 0.173 1524 Planarity : 0.004 0.040 1778 Dihedral : 7.683 135.593 1388 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.74 % Allowed : 11.61 % Favored : 87.65 % 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: 1.24 (0.25), residues: 1224 helix: 1.05 (0.22), residues: 592 sheet: 1.28 (0.38), residues: 159 loop : 0.58 (0.30), residues: 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 82 average time/residue: 0.2066 time to fit residues: 25.4972 Evaluate side-chains 68 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1201 time to fit residues: 1.9805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10328 Z= 0.224 Angle : 0.586 9.355 13951 Z= 0.289 Chirality : 0.041 0.161 1524 Planarity : 0.004 0.039 1778 Dihedral : 7.465 129.568 1388 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.28 % Allowed : 12.35 % Favored : 87.37 % 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: 1.37 (0.25), residues: 1224 helix: 1.22 (0.23), residues: 585 sheet: 1.27 (0.37), residues: 166 loop : 0.56 (0.30), residues: 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 79 average time/residue: 0.2270 time to fit residues: 26.3495 Evaluate side-chains 71 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0959 time to fit residues: 1.8789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10328 Z= 0.273 Angle : 0.621 10.103 13951 Z= 0.302 Chirality : 0.041 0.161 1524 Planarity : 0.004 0.039 1778 Dihedral : 7.425 124.648 1388 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.56 % Allowed : 13.28 % Favored : 86.17 % 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 (0.25), residues: 1224 helix: 1.16 (0.22), residues: 588 sheet: 1.01 (0.38), residues: 167 loop : 0.42 (0.30), residues: 469 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 0.2259 time to fit residues: 25.4899 Evaluate side-chains 70 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1135 time to fit residues: 2.4346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10328 Z= 0.188 Angle : 0.606 13.271 13951 Z= 0.288 Chirality : 0.040 0.224 1524 Planarity : 0.004 0.038 1778 Dihedral : 7.167 119.508 1388 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.09 % Allowed : 13.37 % Favored : 86.54 % 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: 1.33 (0.25), residues: 1224 helix: 1.28 (0.23), residues: 583 sheet: 1.04 (0.37), residues: 172 loop : 0.50 (0.30), residues: 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2242 time to fit residues: 24.9478 Evaluate side-chains 68 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10328 Z= 0.196 Angle : 0.643 13.759 13951 Z= 0.305 Chirality : 0.040 0.172 1524 Planarity : 0.004 0.038 1778 Dihedral : 7.031 114.780 1388 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.37 % Allowed : 13.93 % Favored : 85.70 % 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: 1.37 (0.25), residues: 1224 helix: 1.32 (0.23), residues: 583 sheet: 1.08 (0.37), residues: 172 loop : 0.49 (0.30), residues: 469 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 74 average time/residue: 0.1962 time to fit residues: 23.1185 Evaluate side-chains 68 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1225 time to fit residues: 1.7168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 113 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10328 Z= 0.162 Angle : 0.636 12.998 13951 Z= 0.297 Chirality : 0.039 0.165 1524 Planarity : 0.004 0.039 1778 Dihedral : 6.816 112.612 1388 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.19 % Allowed : 14.21 % Favored : 85.61 % 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 (0.25), residues: 1224 helix: 1.37 (0.23), residues: 587 sheet: 1.11 (0.37), residues: 173 loop : 0.46 (0.30), residues: 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 0.1994 time to fit residues: 24.2458 Evaluate side-chains 71 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1182 time to fit residues: 2.1357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 0.0010 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.072026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.051994 restraints weight = 38364.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053920 restraints weight = 18510.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.055164 restraints weight = 11401.454| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10328 Z= 0.181 Angle : 0.635 11.822 13951 Z= 0.299 Chirality : 0.040 0.166 1524 Planarity : 0.004 0.038 1778 Dihedral : 6.785 110.756 1388 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1224 helix: 1.36 (0.23), residues: 587 sheet: 1.13 (0.37), residues: 173 loop : 0.44 (0.30), residues: 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1916.90 seconds wall clock time: 35 minutes 45.36 seconds (2145.36 seconds total)