Starting phenix.real_space_refine (version: 1.21rc1) on Fri May 12 22:04:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szk_25571/05_2023/7szk_25571_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szk_25571/05_2023/7szk_25571.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szk_25571/05_2023/7szk_25571_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szk_25571/05_2023/7szk_25571_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szk_25571/05_2023/7szk_25571_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szk_25571/05_2023/7szk_25571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szk_25571/05_2023/7szk_25571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szk_25571/05_2023/7szk_25571_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szk_25571/05_2023/7szk_25571_trim_updated.pdb" } resolution = 2.94 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= 0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 18547 2.51 5 N 5260 2.21 5 O 5785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 67": "OE1" <-> "OE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 340": "OD1" <-> "OD2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 790": "OD1" <-> "OD2" Residue "C GLU 835": "OE1" <-> "OE2" Residue "C ASP 853": "OD1" <-> "OD2" Residue "C GLU 898": "OE1" <-> "OE2" Residue "C PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 937": "OD1" <-> "OD2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 29759 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "D" Number of atoms: 10382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10382 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 4, 'PTRANS': 55, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3799 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 14, 'TRANS': 451} Chain breaks: 3 Chain: "X" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "Y" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 82 Unusual residues: {'D9X': 1} Classifications: {'undetermined': 1} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14615 SG CYS D 70 43.056 116.702 81.360 1.00141.16 S ATOM 14629 SG CYS D 72 43.095 117.516 85.168 1.00154.90 S ATOM 14737 SG CYS D 85 42.223 120.160 82.792 1.00153.37 S ATOM 14761 SG CYS D 88 45.709 118.966 82.987 1.00148.93 S ATOM 20449 SG CYS D 814 80.257 95.912 27.490 1.00 56.35 S ATOM 21014 SG CYS D 888 81.014 95.978 31.119 1.00 53.92 S ATOM 21065 SG CYS D 895 78.939 93.224 29.725 1.00 45.54 S ATOM 21086 SG CYS D 898 82.576 93.415 28.949 1.00 47.58 S Time building chain proxies: 15.71, per 1000 atoms: 0.53 Number of scatterers: 29759 At special positions: 0 Unit cell: (173.6, 191.52, 165.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 36 15.00 Mg 1 11.99 O 5785 8.00 N 5260 7.00 C 18547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.01 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " Number of angles added : 12 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 129 helices and 33 sheets defined 38.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.840A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 213 through 232 removed outlier: 4.419A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 213 through 232 removed outlier: 4.372A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 289 through 292 No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.977A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 456 through 481 Processing helix chain 'C' and resid 496 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 608 through 613 removed outlier: 4.248A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 663 through 666 No H-bonds generated for 'chain 'C' and resid 663 through 666' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 688 removed outlier: 4.241A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 821 through 824 No H-bonds generated for 'chain 'C' and resid 821 through 824' Processing helix chain 'C' and resid 859 through 862 No H-bonds generated for 'chain 'C' and resid 859 through 862' Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 980 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 994 through 999 removed outlier: 4.197A pdb=" N LEU C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 994 through 999' Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1082 through 1084 No H-bonds generated for 'chain 'C' and resid 1082 through 1084' Processing helix chain 'C' and resid 1100 through 1104 removed outlier: 3.757A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) Proline residue: C1104 - end of helix No H-bonds generated for 'chain 'C' and resid 1100 through 1104' Processing helix chain 'C' and resid 1110 through 1133 Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1167 through 1178 removed outlier: 4.945A pdb=" N LYS C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1272 through 1280 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1310 Processing helix chain 'C' and resid 1321 through 1332 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 95 through 99 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 123 through 127 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 285 Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.867A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 415 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 removed outlier: 4.286A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 483 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.990A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 615 through 635 Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 650 through 670 removed outlier: 3.736A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 703 removed outlier: 4.050A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 803 removed outlier: 4.038A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 885 through 887 No H-bonds generated for 'chain 'D' and resid 885 through 887' Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 915 through 929 Proline residue: D 926 - end of helix removed outlier: 5.804A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 Processing helix chain 'D' and resid 1217 through 1224 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 4.633A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1280 through 1292 Processing helix chain 'D' and resid 1309 through 1315 Processing helix chain 'D' and resid 1319 through 1325 removed outlier: 3.599A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1338 Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1363 through 1372 Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 61 through 76 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 113 through 136 removed outlier: 3.640A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 153 Processing helix chain 'F' and resid 158 through 161 No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 214 through 233 Processing helix chain 'F' and resid 244 through 258 Processing helix chain 'F' and resid 263 through 295 removed outlier: 4.441A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 314 through 321 Processing helix chain 'F' and resid 325 through 351 removed outlier: 4.132A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 393 removed outlier: 4.817A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 417 Processing helix chain 'F' and resid 427 through 445 Processing helix chain 'F' and resid 454 through 474 Processing helix chain 'F' and resid 480 through 486 Processing helix chain 'F' and resid 493 through 499 Processing helix chain 'F' and resid 519 through 522 Processing helix chain 'F' and resid 531 through 550 Processing helix chain 'F' and resid 553 through 562 Processing helix chain 'F' and resid 573 through 579 Processing helix chain 'F' and resid 585 through 599 Processing helix chain 'F' and resid 605 through 610 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 28 removed outlier: 3.752A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.892A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.628A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.514A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 170 through 172 removed outlier: 7.046A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.620A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 13 through 15 Processing sheet with id= H, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'C' and resid 115 through 117 removed outlier: 3.585A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 143 through 145 Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'C' and resid 173 through 176 removed outlier: 3.585A pdb=" N PHE C 186 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 229 through 231 Processing sheet with id= N, first strand: chain 'C' and resid 603 through 606 Processing sheet with id= O, first strand: chain 'C' and resid 634 through 637 Processing sheet with id= P, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.060A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1226 through 1232 removed outlier: 4.567A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= S, first strand: chain 'C' and resid 1065 through 1067 Processing sheet with id= T, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.227A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.549A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 103 through 106 removed outlier: 3.578A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 446 through 448 removed outlier: 7.705A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 547 through 556 Processing sheet with id= Y, first strand: chain 'D' and resid 706 through 708 Processing sheet with id= Z, first strand: chain 'D' and resid 820 through 823 Processing sheet with id= AA, first strand: chain 'D' and resid 959 through 961 removed outlier: 4.098A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AC, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 3.586A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id= AE, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id= AF, first strand: chain 'D' and resid 825 through 827 removed outlier: 3.566A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.651A pdb=" N ILE D 950 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG 1072 hydrogen bonds defined for protein. 3141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.71 Time building geometry restraints manager: 13.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5130 1.31 - 1.43: 7109 1.43 - 1.56: 17723 1.56 - 1.68: 87 1.68 - 1.81: 225 Bond restraints: 30274 Sorted by residual: bond pdb=" C10 D9X C3001 " pdb=" C11 D9X C3001 " ideal model delta sigma weight residual 0.000 1.537 -1.537 2.00e-02 2.50e+03 5.91e+03 bond pdb=" C09 D9X C3001 " pdb=" C10 D9X C3001 " ideal model delta sigma weight residual 2.341 1.339 1.002 2.00e-02 2.50e+03 2.51e+03 bond pdb=" C42 D9X C3001 " pdb=" C81 D9X C3001 " ideal model delta sigma weight residual 0.833 1.543 -0.710 2.00e-02 2.50e+03 1.26e+03 bond pdb=" C21 D9X C3001 " pdb=" C22 D9X C3001 " ideal model delta sigma weight residual 1.972 1.341 0.631 2.00e-02 2.50e+03 9.97e+02 bond pdb=" C09 D9X C3001 " pdb=" O08 D9X C3001 " ideal model delta sigma weight residual 2.041 1.437 0.604 2.00e-02 2.50e+03 9.11e+02 ... (remaining 30269 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.78: 958 106.78 - 113.58: 16854 113.58 - 120.38: 11224 120.38 - 127.19: 11720 127.19 - 133.99: 271 Bond angle restraints: 41027 Sorted by residual: angle pdb=" C43 D9X C3001 " pdb=" C44 D9X C3001 " pdb=" C78 D9X C3001 " ideal model delta sigma weight residual 29.89 117.91 -88.02 3.00e+00 1.11e-01 8.61e+02 angle pdb=" C46 D9X C3001 " pdb=" C47 D9X C3001 " pdb=" O48 D9X C3001 " ideal model delta sigma weight residual 81.69 121.96 -40.27 3.00e+00 1.11e-01 1.80e+02 angle pdb=" C21 D9X C3001 " pdb=" C22 D9X C3001 " pdb=" C23 D9X C3001 " ideal model delta sigma weight residual 154.73 120.08 34.65 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C20 D9X C3001 " pdb=" C21 D9X C3001 " pdb=" C22 D9X C3001 " ideal model delta sigma weight residual 86.09 120.29 -34.20 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C10 D9X C3001 " pdb=" C09 D9X C3001 " pdb=" O08 D9X C3001 " ideal model delta sigma weight residual 154.14 120.29 33.85 3.00e+00 1.11e-01 1.27e+02 ... (remaining 41022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.18: 17551 26.18 - 52.36: 864 52.36 - 78.54: 109 78.54 - 104.72: 11 104.72 - 130.90: 2 Dihedral angle restraints: 18537 sinusoidal: 7933 harmonic: 10604 Sorted by residual: dihedral pdb=" CA LEU D1344 " pdb=" C LEU D1344 " pdb=" N ARG D1345 " pdb=" CA ARG D1345 " ideal model delta harmonic sigma weight residual 180.00 142.94 37.06 0 5.00e+00 4.00e-02 5.50e+01 dihedral pdb=" CA ASP C1160 " pdb=" C ASP C1160 " pdb=" N LEU C1161 " pdb=" CA LEU C1161 " ideal model delta harmonic sigma weight residual 0.00 26.69 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual 180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 18534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.565: 4671 0.565 - 1.130: 0 1.130 - 1.695: 0 1.695 - 2.260: 0 2.260 - 2.825: 2 Chirality restraints: 4673 Sorted by residual: chirality pdb=" C78 D9X C3001 " pdb=" C44 D9X C3001 " pdb=" C79 D9X C3001 " pdb=" O77 D9X C3001 " both_signs ideal model delta sigma weight residual False -2.83 -0.00 -2.82 2.00e-01 2.50e+01 2.00e+02 chirality pdb=" C79 D9X C3001 " pdb=" C78 D9X C3001 " pdb=" C81 D9X C3001 " pdb=" N80 D9X C3001 " both_signs ideal model delta sigma weight residual False 2.50 0.04 2.47 2.00e-01 2.50e+01 1.52e+02 chirality pdb=" C13 D9X C3001 " pdb=" C12 D9X C3001 " pdb=" C14 D9X C3001 " pdb=" O31 D9X C3001 " both_signs ideal model delta sigma weight residual False 2.67 2.51 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 4670 not shown) Planarity restraints: 5242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 120 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO D 121 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 697 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO C 698 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 698 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 698 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 10 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO B 11 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 11 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 11 " -0.023 5.00e-02 4.00e+02 ... (remaining 5239 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 288 2.57 - 3.15: 25367 3.15 - 3.73: 43911 3.73 - 4.32: 60683 4.32 - 4.90: 103126 Nonbonded interactions: 233375 Sorted by model distance: nonbonded pdb=" O LEU F 250 " pdb=" OG SER F 253 " model vdw 1.985 2.440 nonbonded pdb=" O LYS D 964 " pdb=" OG1 THR D 976 " model vdw 2.006 2.440 nonbonded pdb=" OE1 GLU D 811 " pdb=" OG1 THR D 890 " model vdw 2.032 2.440 nonbonded pdb=" OE1 GLN D1044 " pdb=" OG1 THR D1045 " model vdw 2.034 2.440 nonbonded pdb=" O LYS F 418 " pdb=" OH TYR F 430 " model vdw 2.041 2.440 ... (remaining 233370 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 235) selection = (chain 'B' and resid 7 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 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: 0.030 Extract box with map and model: 12.520 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 80.590 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.015 1.537 30274 Z= 1.039 Angle : 0.792 88.016 41027 Z= 0.327 Chirality : 0.067 2.825 4673 Planarity : 0.003 0.056 5242 Dihedral : 14.667 130.900 11701 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 31.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.28 (0.14), residues: 3661 helix: 2.25 (0.14), residues: 1465 sheet: -0.31 (0.27), residues: 417 loop : -1.56 (0.14), residues: 1779 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 3.293 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 1.6792 time to fit residues: 677.1442 Evaluate side-chains 254 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 3.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 289 optimal weight: 0.0270 chunk 111 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 335 optimal weight: 20.0000 overall best weight: 0.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS C 83 GLN C 327 GLN C1324 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN E 43 ASN E 62 GLN E 70 GLN F 545 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 30274 Z= 0.264 Angle : 0.768 46.222 41027 Z= 0.359 Chirality : 0.045 0.454 4673 Planarity : 0.005 0.044 5242 Dihedral : 11.082 140.971 4422 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.10 (0.14), residues: 3661 helix: 1.93 (0.14), residues: 1465 sheet: -0.29 (0.27), residues: 408 loop : -1.51 (0.14), residues: 1788 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 269 time to evaluate : 3.756 Fit side-chains outliers start: 61 outliers final: 15 residues processed: 299 average time/residue: 1.6258 time to fit residues: 567.0089 Evaluate side-chains 267 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 252 time to evaluate : 3.599 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 7 average time/residue: 0.3631 time to fit residues: 9.2975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 335 optimal weight: 6.9990 chunk 362 optimal weight: 9.9990 chunk 298 optimal weight: 0.9980 chunk 332 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1324 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 ASN E 43 ASN E 70 GLN ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 30274 Z= 0.265 Angle : 0.768 46.222 41027 Z= 0.359 Chirality : 0.045 0.454 4673 Planarity : 0.005 0.076 5242 Dihedral : 11.082 140.971 4422 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.10 (0.14), residues: 3661 helix: 1.93 (0.14), residues: 1465 sheet: -0.29 (0.27), residues: 408 loop : -1.51 (0.14), residues: 1788 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 3.909 Fit side-chains outliers start: 8 outliers final: 9 residues processed: 260 average time/residue: 1.6414 time to fit residues: 500.0299 Evaluate side-chains 256 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 3.549 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 4.7737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 336 optimal weight: 0.0470 chunk 356 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 319 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 70 GLN ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 30274 Z= 0.265 Angle : 0.768 46.221 41027 Z= 0.359 Chirality : 0.045 0.453 4673 Planarity : 0.005 0.076 5242 Dihedral : 11.082 140.962 4422 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.10 (0.14), residues: 3661 helix: 1.93 (0.14), residues: 1465 sheet: -0.29 (0.27), residues: 408 loop : -1.51 (0.14), residues: 1788 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 3.836 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 256 average time/residue: 1.5878 time to fit residues: 475.0578 Evaluate side-chains 256 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 3.434 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 4.8374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 5 optimal weight: 0.0270 chunk 265 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 320 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 70 GLN ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 30274 Z= 0.268 Angle : 0.770 46.211 41027 Z= 0.359 Chirality : 0.045 0.448 4673 Planarity : 0.005 0.076 5242 Dihedral : 11.081 140.749 4422 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.10 (0.14), residues: 3661 helix: 1.92 (0.14), residues: 1465 sheet: -0.29 (0.27), residues: 408 loop : -1.51 (0.14), residues: 1788 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 248 time to evaluate : 4.087 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 257 average time/residue: 1.6464 time to fit residues: 496.7898 Evaluate side-chains 256 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 3.811 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 5.2641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 3.9990 chunk 321 optimal weight: 0.0980 chunk 70 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 357 optimal weight: 0.0010 chunk 296 optimal weight: 9.9990 chunk 165 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 70 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 30274 Z= 0.216 Angle : 0.718 46.620 41027 Z= 0.333 Chirality : 0.043 0.254 4673 Planarity : 0.004 0.064 5242 Dihedral : 11.062 138.287 4422 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.10 (0.14), residues: 3661 helix: 1.89 (0.14), residues: 1465 sheet: -0.20 (0.26), residues: 435 loop : -1.51 (0.14), residues: 1761 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 266 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 17 residues processed: 291 average time/residue: 1.6667 time to fit residues: 570.6152 Evaluate side-chains 270 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 253 time to evaluate : 3.702 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.6907 time to fit residues: 8.1678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 0.9990 chunk 40 optimal weight: 0.0000 chunk 203 optimal weight: 0.4980 chunk 260 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 355 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 164 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 490 GLN ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN D 320 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 62 GLN E 70 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 30274 Z= 0.216 Angle : 0.720 46.620 41027 Z= 0.334 Chirality : 0.043 0.253 4673 Planarity : 0.004 0.086 5242 Dihedral : 11.062 138.280 4422 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.10 (0.14), residues: 3661 helix: 1.89 (0.14), residues: 1465 sheet: -0.20 (0.26), residues: 435 loop : -1.51 (0.14), residues: 1761 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 253 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 267 average time/residue: 1.6440 time to fit residues: 516.6520 Evaluate side-chains 265 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 251 time to evaluate : 3.463 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 1 average time/residue: 0.4332 time to fit residues: 5.5971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 242 optimal weight: 0.4980 chunk 175 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 279 optimal weight: 8.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 490 GLN ** C1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 62 GLN E 70 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.128 30274 Z= 0.232 Angle : 0.716 46.605 41027 Z= 0.334 Chirality : 0.043 0.340 4673 Planarity : 0.004 0.085 5242 Dihedral : 11.062 138.157 4422 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.11 (0.14), residues: 3661 helix: 1.89 (0.14), residues: 1465 sheet: -0.20 (0.26), residues: 435 loop : -1.51 (0.14), residues: 1761 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 251 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 267 average time/residue: 1.6529 time to fit residues: 515.2429 Evaluate side-chains 265 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 250 time to evaluate : 3.560 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 1 average time/residue: 0.4352 time to fit residues: 5.7069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 7.9990 chunk 340 optimal weight: 30.0000 chunk 310 optimal weight: 0.1980 chunk 331 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 144 optimal weight: 0.7980 chunk 260 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 299 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 490 GLN C1236 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 62 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.269 30274 Z= 0.292 Angle : 0.737 46.135 41027 Z= 0.343 Chirality : 0.044 0.448 4673 Planarity : 0.004 0.080 5242 Dihedral : 11.061 137.361 4422 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.17 % 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: 0.08 (0.14), residues: 3661 helix: 1.85 (0.14), residues: 1465 sheet: -0.19 (0.26), residues: 435 loop : -1.52 (0.14), residues: 1761 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 250 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 268 average time/residue: 1.6002 time to fit residues: 504.0291 Evaluate side-chains 263 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 245 time to evaluate : 3.661 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 3 average time/residue: 0.8566 time to fit residues: 8.2855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 0.5980 chunk 350 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 166 optimal weight: 0.0870 chunk 243 optimal weight: 0.8980 chunk 367 optimal weight: 10.0000 chunk 338 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: