Starting phenix.real_space_refine (version: dev) on Sun Feb 26 22:19:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye2_33762/02_2023/7ye2_33762_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye2_33762/02_2023/7ye2_33762.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye2_33762/02_2023/7ye2_33762_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye2_33762/02_2023/7ye2_33762_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye2_33762/02_2023/7ye2_33762_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye2_33762/02_2023/7ye2_33762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye2_33762/02_2023/7ye2_33762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye2_33762/02_2023/7ye2_33762_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye2_33762/02_2023/7ye2_33762_updated.pdb" } resolution = 3.8 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= 0.003 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 "A ARG 36": "NH1" <-> "NH2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 573": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C GLU 655": "OE1" <-> "OE2" Residue "C GLU 732": "OE1" <-> "OE2" Residue "C GLU 746": "OE1" <-> "OE2" Residue "C ARG 751": "NH1" <-> "NH2" Residue "C ARG 782": "NH1" <-> "NH2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 843": "OE1" <-> "OE2" Residue "C GLU 904": "OE1" <-> "OE2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C GLU 1038": "OE1" <-> "OE2" Residue "C GLU 1048": "OE1" <-> "OE2" Residue "C GLU 1151": "OE1" <-> "OE2" Residue "C GLU 1175": "OE1" <-> "OE2" Residue "C GLU 1293": "OE1" <-> "OE2" Residue "C GLU 1335": "OE1" <-> "OE2" Residue "C GLU 1343": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 420": "OE1" <-> "OE2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D GLU 767": "OE1" <-> "OE2" Residue "D GLU 1134": "OE1" <-> "OE2" Residue "D GLU 1137": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F GLU 411": "OE1" <-> "OE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F GLU 522": "OE1" <-> "OE2" Residue "F GLU 543": "OE1" <-> "OE2" Residue "F GLU 564": "OE1" <-> "OE2" Residue "F GLU 582": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 28925 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2054 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 191 Chain: "B" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1633 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 206} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 11, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 9603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1303, 9603 Classifications: {'peptide': 1303} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 61, 'TRANS': 1241} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 664 Unresolved non-hydrogen angles: 893 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 18, 'ARG:plan': 87} Unresolved non-hydrogen planarities: 462 Chain: "D" Number of atoms: 8691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8691 Classifications: {'peptide': 1140} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 52, 'TRANS': 1087} Chain breaks: 5 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 73, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 199 Chain: "E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 510 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 3266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3266 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 12, 'TRANS': 484} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 740 Unresolved non-hydrogen angles: 952 Unresolved non-hydrogen dihedrals: 590 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 26, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 457 Chain: "H" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1396 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "I" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1396 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "G" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 372 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19357 SG CYS D 810 96.069 60.412 109.026 1.00 49.86 S ATOM 19883 SG CYS D 884 96.720 63.339 104.845 1.00 36.85 S ATOM 19946 SG CYS D 894 95.931 63.847 108.310 1.00 29.07 S ATOM 13735 SG CYS D 71 81.560 39.659 51.376 1.00 42.92 S ATOM 13749 SG CYS D 73 81.323 39.653 45.835 1.00 52.29 S ATOM 13850 SG CYS D 86 83.437 37.678 48.156 1.00 45.01 S ATOM 28641 SG CYS G 118 141.652 52.766 33.401 1.00 85.71 S ATOM 28758 SG CYS G 133 142.995 52.390 30.132 1.00 93.25 S ATOM 28825 SG CYS G 143 143.210 55.974 32.776 1.00 81.95 S Time building chain proxies: 16.59, per 1000 atoms: 0.57 Number of scatterers: 28925 At special positions: 0 Unit cell: (176, 145, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 106 16.00 P 136 15.00 Mg 1 11.99 O 5797 8.00 N 4893 7.00 C 17977 6.00 H 12 1.00 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: 12.84 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 894 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 884 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 810 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 86 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 71 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 146 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 118 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 143 " Number of angles added : 3 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 22 sheets defined 36.5% alpha, 4.6% beta 48 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 11.20 Creating SS restraints... Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.971A pdb=" N ALA A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 removed outlier: 3.972A pdb=" N ASN A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'B' and resid 38 through 50 removed outlier: 3.520A pdb=" N VAL B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.536A pdb=" N VAL B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 38 removed outlier: 4.109A pdb=" N VAL C 30 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 31 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 32 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 33 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 36 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 53 through 60 Processing helix chain 'C' and resid 86 through 92 removed outlier: 4.180A pdb=" N GLN C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 277 through 285 removed outlier: 3.773A pdb=" N GLN C 281 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.696A pdb=" N ALA C 334 " --> pdb=" O ILE C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 334' Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.722A pdb=" N ARG C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 378 Processing helix chain 'C' and resid 386 through 396 removed outlier: 3.572A pdb=" N GLU C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 416 Processing helix chain 'C' and resid 430 through 445 removed outlier: 3.724A pdb=" N LEU C 434 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 487 Processing helix chain 'C' and resid 504 through 515 removed outlier: 3.890A pdb=" N VAL C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 535 Processing helix chain 'C' and resid 552 through 555 No H-bonds generated for 'chain 'C' and resid 552 through 555' Processing helix chain 'C' and resid 560 through 562 No H-bonds generated for 'chain 'C' and resid 560 through 562' Processing helix chain 'C' and resid 664 through 666 No H-bonds generated for 'chain 'C' and resid 664 through 666' Processing helix chain 'C' and resid 670 through 673 No H-bonds generated for 'chain 'C' and resid 670 through 673' Processing helix chain 'C' and resid 685 through 693 Processing helix chain 'C' and resid 710 through 717 Processing helix chain 'C' and resid 826 through 830 removed outlier: 3.682A pdb=" N ARG C 830 " --> pdb=" O ARG C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 912 Processing helix chain 'C' and resid 952 through 987 removed outlier: 3.985A pdb=" N GLY C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1008 through 1010 No H-bonds generated for 'chain 'C' and resid 1008 through 1010' Processing helix chain 'C' and resid 1024 through 1056 Processing helix chain 'C' and resid 1118 through 1123 Proline residue: C1122 - end of helix Processing helix chain 'C' and resid 1127 through 1150 Processing helix chain 'C' and resid 1157 through 1166 removed outlier: 4.117A pdb=" N ALA C1161 " --> pdb=" O GLY C1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 1183 through 1192 removed outlier: 3.705A pdb=" N ARG C1188 " --> pdb=" O VAL C1184 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS C1192 " --> pdb=" O ARG C1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1215 Processing helix chain 'C' and resid 1286 through 1294 removed outlier: 4.010A pdb=" N ALA C1291 " --> pdb=" O MET C1287 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU C1292 " --> pdb=" O GLU C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1298 through 1304 Processing helix chain 'C' and resid 1312 through 1324 removed outlier: 4.199A pdb=" N THR C1316 " --> pdb=" O VAL C1312 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS C1317 " --> pdb=" O ALA C1313 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1346 Processing helix chain 'D' and resid 28 through 34 Processing helix chain 'D' and resid 60 through 63 No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 133 through 140 removed outlier: 3.684A pdb=" N ARG D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 168 No H-bonds generated for 'chain 'D' and resid 165 through 168' Processing helix chain 'D' and resid 184 through 193 Processing helix chain 'D' and resid 196 through 207 Processing helix chain 'D' and resid 215 through 232 removed outlier: 4.028A pdb=" N LYS D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 266 through 287 Processing helix chain 'D' and resid 291 through 309 Processing helix chain 'D' and resid 329 through 334 removed outlier: 3.905A pdb=" N LEU D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 378 removed outlier: 3.536A pdb=" N LEU D 376 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 390 Processing helix chain 'D' and resid 396 through 404 Processing helix chain 'D' and resid 408 through 417 removed outlier: 4.235A pdb=" N ASP D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D 413 " --> pdb=" O GLN D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 453 through 459 removed outlier: 4.174A pdb=" N ALA D 457 " --> pdb=" O PRO D 453 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 484 removed outlier: 3.894A pdb=" N ARG D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 490 No H-bonds generated for 'chain 'D' and resid 488 through 490' Processing helix chain 'D' and resid 507 through 516 Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.787A pdb=" N GLU D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.799A pdb=" N ILE D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 592 No H-bonds generated for 'chain 'D' and resid 589 through 592' Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 614 through 633 Processing helix chain 'D' and resid 648 through 663 removed outlier: 4.346A pdb=" N THR D 651 " --> pdb=" O VAL D 648 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ALA D 652 " --> pdb=" O ARG D 649 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 661 " --> pdb=" O ARG D 658 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 663 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 682 Processing helix chain 'D' and resid 690 through 702 Processing helix chain 'D' and resid 717 through 724 Processing helix chain 'D' and resid 730 through 736 Processing helix chain 'D' and resid 765 through 799 removed outlier: 4.251A pdb=" N LYS D 777 " --> pdb=" O HIS D 773 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY D 778 " --> pdb=" O GLY D 774 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR D 786 " --> pdb=" O THR D 782 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA D 787 " --> pdb=" O ALA D 783 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 788 " --> pdb=" O LEU D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 834 No H-bonds generated for 'chain 'D' and resid 831 through 834' Processing helix chain 'D' and resid 862 through 870 Processing helix chain 'D' and resid 892 through 895 No H-bonds generated for 'chain 'D' and resid 892 through 895' Processing helix chain 'D' and resid 911 through 921 Processing helix chain 'D' and resid 1129 through 1137 Processing helix chain 'D' and resid 1213 through 1219 Processing helix chain 'D' and resid 1222 through 1240 Processing helix chain 'D' and resid 1246 through 1257 removed outlier: 3.806A pdb=" N ILE D1252 " --> pdb=" O HIS D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1276 through 1288 removed outlier: 4.335A pdb=" N GLU D1284 " --> pdb=" O GLU D1280 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS D1287 " --> pdb=" O LYS D1283 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D1288 " --> pdb=" O GLU D1284 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1321 No H-bonds generated for 'chain 'D' and resid 1318 through 1321' Processing helix chain 'D' and resid 1327 through 1332 Processing helix chain 'D' and resid 1343 through 1349 Processing helix chain 'D' and resid 1357 through 1378 Processing helix chain 'E' and resid 7 through 10 No H-bonds generated for 'chain 'E' and resid 7 through 10' Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.790A pdb=" N SER E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 4.868A pdb=" N ALA E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 3.949A pdb=" N GLU E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 125 Processing helix chain 'F' and resid 134 through 152 Processing helix chain 'F' and resid 157 through 168 removed outlier: 3.771A pdb=" N GLU F 168 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 188 removed outlier: 3.643A pdb=" N TYR F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 274 removed outlier: 4.861A pdb=" N SER F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU F 257 " --> pdb=" O ALA F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 300 removed outlier: 3.551A pdb=" N THR F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 293 " --> pdb=" O LEU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 332 removed outlier: 3.627A pdb=" N ALA F 309 " --> pdb=" O ASN F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 4.093A pdb=" N LYS F 344 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 370 removed outlier: 3.503A pdb=" N LYS F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 390 removed outlier: 3.567A pdb=" N ASP F 379 " --> pdb=" O GLN F 375 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU F 390 " --> pdb=" O ALA F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 421 Processing helix chain 'F' and resid 424 through 432 removed outlier: 4.007A pdb=" N LYS F 432 " --> pdb=" O ILE F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 456 removed outlier: 4.046A pdb=" N ILE F 450 " --> pdb=" O GLN F 446 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 483 Processing helix chain 'F' and resid 494 through 513 Processing helix chain 'F' and resid 520 through 526 removed outlier: 3.588A pdb=" N ALA F 524 " --> pdb=" O PRO F 520 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU F 525 " --> pdb=" O GLU F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 537 Processing helix chain 'F' and resid 559 through 561 No H-bonds generated for 'chain 'F' and resid 559 through 561' Processing helix chain 'F' and resid 571 through 588 Processing helix chain 'F' and resid 593 through 603 removed outlier: 3.515A pdb=" N PHE F 603 " --> pdb=" O LEU F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 618 Processing helix chain 'F' and resid 625 through 639 removed outlier: 4.289A pdb=" N LYS F 639 " --> pdb=" O LEU F 635 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 150 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.730A pdb=" N TYR A 198 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 104 through 107 removed outlier: 3.932A pdb=" N ALA A 107 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 142 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= D, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.629A pdb=" N ARG B 94 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU B 125 " --> pdb=" O ARG B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= F, first strand: chain 'B' and resid 186 through 188 removed outlier: 4.075A pdb=" N GLU B 187 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 71 through 74 removed outlier: 4.075A pdb=" N VAL C 71 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 107 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY C 131 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL C 102 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR C 129 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 104 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP C 127 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 77 through 79 Processing sheet with id= I, first strand: chain 'C' and resid 160 through 164 Processing sheet with id= J, first strand: chain 'C' and resid 611 through 615 removed outlier: 3.708A pdb=" N SER C 597 " --> pdb=" O MET C 614 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 738 through 741 Processing sheet with id= L, first strand: chain 'C' and resid 805 through 809 Processing sheet with id= M, first strand: chain 'C' and resid 842 through 844 Processing sheet with id= N, first strand: chain 'C' and resid 893 through 895 removed outlier: 3.902A pdb=" N THR C 894 " --> pdb=" O ARG C 920 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 642 through 646 removed outlier: 3.795A pdb=" N ILE C 645 " --> pdb=" O GLU C 648 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU C 648 " --> pdb=" O ILE C 645 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 104 through 107 Processing sheet with id= Q, first strand: chain 'D' and resid 254 through 256 removed outlier: 4.027A pdb=" N VAL D 255 " --> pdb=" O ALA D 263 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.022A pdb=" N SER D 355 " --> pdb=" O MET D 468 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 357 through 359 removed outlier: 5.984A pdb=" N ILE D 449 " --> pdb=" O VAL D 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 369 through 371 removed outlier: 5.552A pdb=" N LYS D 442 " --> pdb=" O LEU D 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 816 through 818 Processing sheet with id= V, first strand: chain 'D' and resid 1259 through 1262 removed outlier: 4.306A pdb=" N LYS D1259 " --> pdb=" O VAL D1301 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 250 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 13.86 Time building geometry restraints manager: 13.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 12 1.05 - 1.24: 3867 1.24 - 1.43: 8096 1.43 - 1.62: 17464 1.62 - 1.81: 194 Bond restraints: 29633 Sorted by residual: bond pdb=" C4' 6MA I -13 " pdb=" C3' 6MA I -13 " ideal model delta sigma weight residual 1.672 1.309 0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C4' 6MA H 11 " pdb=" C3' 6MA H 11 " ideal model delta sigma weight residual 1.672 1.311 0.361 2.00e-02 2.50e+03 3.27e+02 bond pdb=" C4' 6MA I -5 " pdb=" C3' 6MA I -5 " ideal model delta sigma weight residual 1.672 1.313 0.359 2.00e-02 2.50e+03 3.23e+02 bond pdb=" C4' 6MA H 3 " pdb=" C3' 6MA H 3 " ideal model delta sigma weight residual 1.672 1.316 0.356 2.00e-02 2.50e+03 3.18e+02 bond pdb=" C3' 6MA H 3 " pdb=" C2' 6MA H 3 " ideal model delta sigma weight residual 1.232 1.585 -0.353 2.00e-02 2.50e+03 3.11e+02 ... (remaining 29628 not shown) Histogram of bond angle deviations from ideal: 79.72 - 93.64: 2 93.64 - 107.56: 1848 107.56 - 121.48: 31285 121.48 - 135.40: 7488 135.40 - 149.32: 5 Bond angle restraints: 40628 Sorted by residual: angle pdb=" C1' 6MA I -13 " pdb=" N9 6MA I -13 " pdb=" C4 6MA I -13 " ideal model delta sigma weight residual 118.25 149.32 -31.07 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C1' 6MA I -5 " pdb=" N9 6MA I -5 " pdb=" C4 6MA I -5 " ideal model delta sigma weight residual 118.25 149.31 -31.06 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C1' 6MA I -13 " pdb=" N9 6MA I -13 " pdb=" C8 6MA I -13 " ideal model delta sigma weight residual 132.95 102.04 30.91 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C1' 6MA I -5 " pdb=" N9 6MA I -5 " pdb=" C8 6MA I -5 " ideal model delta sigma weight residual 132.95 102.05 30.90 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C1' 6MA H 11 " pdb=" N9 6MA H 11 " pdb=" C4 6MA H 11 " ideal model delta sigma weight residual 118.25 149.13 -30.88 3.00e+00 1.11e-01 1.06e+02 ... (remaining 40623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.53: 16916 34.53 - 69.07: 634 69.07 - 103.60: 37 103.60 - 138.13: 0 138.13 - 172.66: 7 Dihedral angle restraints: 17594 sinusoidal: 7391 harmonic: 10203 Sorted by residual: dihedral pdb=" CG ARG D 776 " pdb=" CD ARG D 776 " pdb=" NE ARG D 776 " pdb=" CZ ARG D 776 " ideal model delta sinusoidal sigma weight residual 90.00 25.46 64.54 2 1.50e+01 4.44e-03 1.74e+01 dihedral pdb=" C4' DC H 19 " pdb=" C3' DC H 19 " pdb=" O3' DC H 19 " pdb=" P DG H 20 " ideal model delta sinusoidal sigma weight residual 220.00 47.34 172.66 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I 24 " pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DC I 25 " ideal model delta sinusoidal sigma weight residual 220.00 47.70 172.30 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 17591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3867 0.045 - 0.089: 685 0.089 - 0.134: 225 0.134 - 0.178: 3 0.178 - 0.223: 4 Chirality restraints: 4784 Sorted by residual: chirality pdb=" C1' 6MA H 11 " pdb=" O4' 6MA H 11 " pdb=" C2' 6MA H 11 " pdb=" N9 6MA H 11 " both_signs ideal model delta sigma weight residual False 2.54 2.31 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C1' 6MA I -13 " pdb=" O4' 6MA I -13 " pdb=" C2' 6MA I -13 " pdb=" N9 6MA I -13 " both_signs ideal model delta sigma weight residual False 2.54 2.32 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C1' 6MA H 3 " pdb=" O4' 6MA H 3 " pdb=" C2' 6MA H 3 " pdb=" N9 6MA H 3 " both_signs ideal model delta sigma weight residual False 2.54 2.35 0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 4781 not shown) Planarity restraints: 4770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 360 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO D 361 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 361 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 361 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 111 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 112 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 29 " 0.010 2.00e-02 2.50e+03 1.04e-02 2.43e+00 pdb=" N1 DC I 29 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DC I 29 " 0.021 2.00e-02 2.50e+03 pdb=" O2 DC I 29 " -0.015 2.00e-02 2.50e+03 pdb=" N3 DC I 29 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 29 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 29 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC I 29 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 29 " -0.006 2.00e-02 2.50e+03 ... (remaining 4767 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.46: 151 2.46 - 2.99: 15212 2.99 - 3.53: 38772 3.53 - 4.06: 52701 4.06 - 4.60: 78450 Nonbonded interactions: 185286 Sorted by model distance: nonbonded pdb=" OE2 GLU C 224 " pdb=" H ALA C 309 " model vdw 1.924 1.850 nonbonded pdb=" OD2 ASP D 466 " pdb="MG MG D2003 " model vdw 2.073 2.050 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D2003 " model vdw 2.121 2.050 nonbonded pdb=" O ASP C1310 " pdb=" N GLU C1335 " model vdw 2.217 2.350 nonbonded pdb=" O ALA F 422 " pdb=" ND2 ASN F 423 " model vdw 2.217 2.350 ... (remaining 185281 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: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 136 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 17977 2.51 5 N 4893 2.21 5 O 5797 1.98 5 H 12 0.53 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=0.84 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: 1.960 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: 0.820 Extract box with map and model: 8.310 Check model and map are aligned: 0.460 Process input model: 89.510 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.300 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.008 0.363 29621 Z= 0.375 Angle : 0.691 31.068 40598 Z= 0.307 Chirality : 0.038 0.223 4784 Planarity : 0.003 0.047 4764 Dihedral : 16.417 172.665 10966 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 47.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer Outliers : 0.35 % 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: -3.04 (0.13), residues: 3544 helix: -0.79 (0.13), residues: 1356 sheet: -3.06 (0.33), residues: 207 loop : -2.93 (0.12), residues: 1981 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 740 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 731 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 738 average time/residue: 0.3956 time to fit residues: 466.4883 Evaluate side-chains 533 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 526 time to evaluate : 3.066 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 7 average time/residue: 0.4739 time to fit residues: 9.0238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 0.8980 chunk 278 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 188 optimal weight: 0.0470 chunk 149 optimal weight: 30.0000 chunk 288 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 GLN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 357 ASN ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 GLN ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 ASN C 814 ASN C 862 ASN C 870 ASN C 941 ASN C 974 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 GLN C1155 GLN ** C1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS D 278 ASN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 ASN ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1275 HIS D1285 GLN E 42 ASN ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 509 GLN F 579 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 29621 Z= 0.317 Angle : 0.573 8.479 40598 Z= 0.303 Chirality : 0.040 0.142 4784 Planarity : 0.003 0.055 4764 Dihedral : 17.705 177.725 4939 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 64.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 3.95 % 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: -1.89 (0.14), residues: 3544 helix: 0.45 (0.14), residues: 1367 sheet: -2.90 (0.35), residues: 205 loop : -2.45 (0.13), residues: 1972 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 642 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 539 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 69 residues processed: 601 average time/residue: 0.3867 time to fit residues: 375.7788 Evaluate side-chains 544 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 475 time to evaluate : 3.211 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 6 residues processed: 69 average time/residue: 0.2899 time to fit residues: 40.3297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 361 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 chunk 331 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1234 GLN ** C1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 HIS ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 HIS ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 GLN ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1255 GLN ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 29621 Z= 0.392 Angle : 0.646 15.333 40598 Z= 0.339 Chirality : 0.042 0.176 4784 Planarity : 0.004 0.053 4764 Dihedral : 17.910 171.683 4939 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 73.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer Outliers : 4.26 % 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: -1.81 (0.14), residues: 3544 helix: 0.47 (0.15), residues: 1383 sheet: -3.15 (0.38), residues: 171 loop : -2.37 (0.13), residues: 1990 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 629 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 518 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 73 residues processed: 582 average time/residue: 0.4005 time to fit residues: 377.3183 Evaluate side-chains 544 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 471 time to evaluate : 3.473 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 9 residues processed: 73 average time/residue: 0.3061 time to fit residues: 44.7834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 159 optimal weight: 0.0470 chunk 224 optimal weight: 0.8980 chunk 335 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 318 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 ASN ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 801 GLN D 874 GLN ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 29621 Z= 0.283 Angle : 0.536 15.477 40598 Z= 0.283 Chirality : 0.039 0.163 4784 Planarity : 0.003 0.043 4764 Dihedral : 17.798 171.349 4939 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 71.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 3544 helix: 0.79 (0.15), residues: 1373 sheet: -3.06 (0.37), residues: 179 loop : -2.30 (0.14), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 588 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 501 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 60 residues processed: 547 average time/residue: 0.3940 time to fit residues: 353.5402 Evaluate side-chains 526 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 466 time to evaluate : 3.213 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 7 residues processed: 60 average time/residue: 0.2937 time to fit residues: 36.0729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 303 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 319 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1270 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1195 HIS ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.067 29621 Z= 0.496 Angle : 0.746 21.373 40598 Z= 0.384 Chirality : 0.044 0.187 4784 Planarity : 0.004 0.050 4764 Dihedral : 18.083 170.132 4939 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 80.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.23 % Favored : 86.77 % Rotamer Outliers : 4.80 % 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: -2.15 (0.14), residues: 3544 helix: 0.13 (0.14), residues: 1401 sheet: -3.05 (0.37), residues: 163 loop : -2.58 (0.13), residues: 1980 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 617 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 492 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 85 residues processed: 566 average time/residue: 0.4118 time to fit residues: 380.8465 Evaluate side-chains 549 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 464 time to evaluate : 3.314 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 8 residues processed: 85 average time/residue: 0.3020 time to fit residues: 51.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 1.9990 chunk 320 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 356 optimal weight: 7.9990 chunk 295 optimal weight: 0.0060 chunk 164 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 186 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1234 GLN ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 HIS ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1255 GLN ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 29621 Z= 0.165 Angle : 0.478 14.086 40598 Z= 0.256 Chirality : 0.038 0.156 4784 Planarity : 0.003 0.048 4764 Dihedral : 17.793 172.560 4939 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 73.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer Outliers : 1.73 % 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: -1.46 (0.15), residues: 3544 helix: 0.93 (0.15), residues: 1378 sheet: -3.25 (0.33), residues: 214 loop : -2.23 (0.14), residues: 1952 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 568 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 523 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 31 residues processed: 545 average time/residue: 0.4039 time to fit residues: 359.0230 Evaluate side-chains 515 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 484 time to evaluate : 3.261 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 8 residues processed: 31 average time/residue: 0.3263 time to fit residues: 21.8982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 354 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 GLN ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1255 GLN ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.102 29621 Z= 0.498 Angle : 0.708 22.075 40598 Z= 0.365 Chirality : 0.043 0.212 4784 Planarity : 0.004 0.051 4764 Dihedral : 18.026 172.762 4939 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 80.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.94 % Favored : 86.06 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.03 (0.14), residues: 3544 helix: 0.33 (0.15), residues: 1390 sheet: -3.23 (0.33), residues: 199 loop : -2.52 (0.14), residues: 1955 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 590 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 486 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 81 residues processed: 536 average time/residue: 0.4148 time to fit residues: 362.0153 Evaluate side-chains 544 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 463 time to evaluate : 3.426 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 9 residues processed: 81 average time/residue: 0.3228 time to fit residues: 51.8698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 211 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 278 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 GLN ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 29621 Z= 0.172 Angle : 0.482 12.392 40598 Z= 0.258 Chirality : 0.038 0.148 4784 Planarity : 0.003 0.050 4764 Dihedral : 17.806 175.479 4939 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 73.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 1.23 % 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: -1.50 (0.15), residues: 3544 helix: 0.88 (0.15), residues: 1388 sheet: -3.27 (0.32), residues: 225 loop : -2.23 (0.14), residues: 1931 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 532 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 500 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 22 residues processed: 522 average time/residue: 0.4174 time to fit residues: 356.7872 Evaluate side-chains 498 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 476 time to evaluate : 3.391 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 9 residues processed: 22 average time/residue: 0.3812 time to fit residues: 18.7232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 40.0000 chunk 339 optimal weight: 0.0060 chunk 310 optimal weight: 7.9990 chunk 330 optimal weight: 0.2980 chunk 198 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 312 optimal weight: 40.0000 chunk 329 optimal weight: 2.9990 overall best weight: 1.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1255 GLN E 42 ASN ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 29621 Z= 0.269 Angle : 0.535 14.773 40598 Z= 0.282 Chirality : 0.039 0.156 4784 Planarity : 0.003 0.053 4764 Dihedral : 17.815 177.790 4939 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 75.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3544 helix: 0.85 (0.15), residues: 1396 sheet: -3.11 (0.33), residues: 214 loop : -2.27 (0.14), residues: 1934 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 533 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 481 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 45 residues processed: 504 average time/residue: 0.4197 time to fit residues: 345.6188 Evaluate side-chains 516 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 471 time to evaluate : 4.262 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 9 residues processed: 45 average time/residue: 0.3733 time to fit residues: 35.9943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 0.0980 chunk 349 optimal weight: 9.9990 chunk 213 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 337 optimal weight: 10.0000 chunk 291 optimal weight: 0.0050 chunk 30 optimal weight: 4.9990 chunk 225 optimal weight: 0.6980 chunk 179 optimal weight: 0.0770 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 GLN ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1255 GLN E 42 ASN ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 29621 Z= 0.132 Angle : 0.450 10.935 40598 Z= 0.241 Chirality : 0.037 0.142 4784 Planarity : 0.003 0.054 4764 Dihedral : 17.658 179.628 4939 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 71.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 0.58 % 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: -1.08 (0.15), residues: 3544 helix: 1.28 (0.15), residues: 1388 sheet: -3.21 (0.32), residues: 225 loop : -2.02 (0.14), residues: 1931 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 514 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 499 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 512 average time/residue: 0.4493 time to fit residues: 380.9478 Evaluate side-chains 485 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 472 time to evaluate : 3.398 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 13 average time/residue: 0.4671 time to fit residues: 14.7980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 292 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 300 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 0.0000 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.175058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142998 restraints weight = 40071.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141211 restraints weight = 58605.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142275 restraints weight = 58984.552| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 29621 Z= 0.281 Angle : 0.545 15.256 40598 Z= 0.285 Chirality : 0.039 0.143 4784 Planarity : 0.003 0.057 4764 Dihedral : 17.714 179.031 4939 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 75.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer Outliers : 1.11 % 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: -1.23 (0.15), residues: 3544 helix: 1.08 (0.15), residues: 1385 sheet: -3.01 (0.34), residues: 214 loop : -2.09 (0.14), residues: 1945 =============================================================================== Job complete usr+sys time: 6740.87 seconds wall clock time: 123 minutes 32.11 seconds (7412.11 seconds total)