Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 12:59:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/10_2023/8eey_28065.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/10_2023/8eey_28065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/10_2023/8eey_28065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/10_2023/8eey_28065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/10_2023/8eey_28065.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/10_2023/8eey_28065.pdb" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 64 5.49 5 S 88 5.16 5 C 12990 2.51 5 N 3675 2.21 5 O 4065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 418": "OE1" <-> "OE2" Residue "E GLU 493": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 1026": "OE1" <-> "OE2" Residue "A GLU 1075": "OE1" <-> "OE2" Residue "A GLU 1106": "OE1" <-> "OE2" Residue "A GLU 1135": "OE1" <-> "OE2" Residue "A GLU 1142": "OE1" <-> "OE2" Residue "A PHE 1277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1285": "OE1" <-> "OE2" Residue "A GLU 1437": "OE1" <-> "OE2" Residue "A GLU 1461": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 589": "OE1" <-> "OE2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 20886 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 4 Chain: "A" Number of atoms: 12493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1544, 12493 Classifications: {'peptide': 1544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 84, 'TRANS': 1459} Chain breaks: 5 Chain: "B" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6102 Classifications: {'peptide': 735} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 705} Chain breaks: 2 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 801 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "D" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 591 Classifications: {'RNA': 28} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 7, 'rna3p': 20} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1591 SG CYS A 86 108.283 62.903 45.935 1.00 79.46 S ATOM 1837 SG CYS A 115 111.694 63.439 44.964 1.00101.35 S ATOM 1899 SG CYS A 123 108.801 65.997 43.831 1.00 88.24 S ATOM 1923 SG CYS A 126 110.019 65.755 47.465 1.00 78.35 S ATOM 4299 SG CYS A 463 79.698 64.258 64.553 1.00 66.28 S ATOM 4361 SG CYS A 472 82.442 62.327 62.644 1.00 48.27 S ATOM 4375 SG CYS A 474 79.015 63.190 60.941 1.00 49.36 S ATOM 4397 SG CYS A 477 81.478 65.783 61.571 1.00 49.30 S ATOM 6215 SG CYS A 706 59.947 66.538 85.373 1.00 58.72 S ATOM 6230 SG CYS A 708 57.091 68.269 83.636 1.00 52.24 S ATOM 6252 SG CYS A 711 60.665 69.312 82.801 1.00 57.35 S ATOM 8144 SG CYS A 965 44.728 95.059 107.529 1.00 44.16 S ATOM 11050 SG CYS A1312 46.774 91.811 107.994 1.00 40.55 S ATOM 11289 SG CYS A1342 43.041 91.677 107.236 1.00 24.45 S ATOM 11307 SG CYS A1345 45.570 92.658 104.584 1.00 40.75 S Time building chain proxies: 10.89, per 1000 atoms: 0.52 Number of scatterers: 20886 At special positions: 0 Unit cell: (131.274, 184.977, 165.087, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 88 16.00 P 64 15.00 O 4065 8.00 N 3675 7.00 C 12990 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: 8.68 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 86 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 126 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 115 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 123 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 477 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 474 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 463 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 472 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 708 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 706 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 711 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1345 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1312 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1342 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 965 " Number of angles added : 21 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4492 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 23 sheets defined 41.7% alpha, 13.8% beta 21 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'E' and resid 411 through 415 removed outlier: 3.717A pdb=" N ILE E 414 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 415 " --> pdb=" O PRO E 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 411 through 415' Processing helix chain 'E' and resid 467 through 479 Processing helix chain 'E' and resid 525 through 542 removed outlier: 3.684A pdb=" N LYS E 534 " --> pdb=" O ARG E 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.693A pdb=" N ARG A 26 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 removed outlier: 3.603A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 123 through 129 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.925A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 302 removed outlier: 5.801A pdb=" N SER A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 344 through 367 removed outlier: 3.631A pdb=" N MET A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.611A pdb=" N ILE A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 643 through 649 removed outlier: 3.572A pdb=" N VAL A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.540A pdb=" N LEU A 832 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.668A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'A' and resid 1055 through 1059 removed outlier: 3.801A pdb=" N LYS A1058 " --> pdb=" O PRO A1055 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A1059 " --> pdb=" O GLN A1056 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1055 through 1059' Processing helix chain 'A' and resid 1060 through 1065 removed outlier: 4.074A pdb=" N ARG A1065 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 Processing helix chain 'A' and resid 1163 through 1168 Processing helix chain 'A' and resid 1179 through 1183 removed outlier: 3.849A pdb=" N ILE A1183 " --> pdb=" O TRP A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 3.553A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.837A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1326 Processing helix chain 'A' and resid 1328 through 1336 removed outlier: 3.510A pdb=" N ARG A1332 " --> pdb=" O PRO A1329 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A1336 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 4.109A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1535 Processing helix chain 'A' and resid 1538 through 1549 removed outlier: 3.548A pdb=" N GLU A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1585 through 1594 removed outlier: 4.742A pdb=" N GLN A1590 " --> pdb=" O LYS A1586 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS A1591 " --> pdb=" O GLU A1587 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.675A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 65 through 88 removed outlier: 3.780A pdb=" N GLY B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 Processing helix chain 'B' and resid 118 through 134 removed outlier: 3.754A pdb=" N LEU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 164 removed outlier: 3.940A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 207 through 222 removed outlier: 4.022A pdb=" N ILE B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.604A pdb=" N ILE B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 278 through 293 Processing helix chain 'B' and resid 296 through 314 removed outlier: 4.539A pdb=" N GLU B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.730A pdb=" N TYR B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 355 through 374 removed outlier: 3.818A pdb=" N ARG B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 395 removed outlier: 3.506A pdb=" N ILE B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 452 through 455 Processing helix chain 'B' and resid 464 through 481 Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 485 through 500 removed outlier: 3.769A pdb=" N GLU B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 520 through 526 Processing helix chain 'B' and resid 527 through 531 Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.547A pdb=" N ASN B 585 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 603 Processing helix chain 'B' and resid 622 through 625 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 675 through 683 Processing helix chain 'B' and resid 696 through 710 removed outlier: 3.607A pdb=" N TYR B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 730 removed outlier: 3.556A pdb=" N GLN B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER B 730 " --> pdb=" O GLU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 Processing sheet with id=AA1, first strand: chain 'E' and resid 419 through 422 Processing sheet with id=AA2, first strand: chain 'E' and resid 444 through 448 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA4, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.664A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA6, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA7, first strand: chain 'A' and resid 106 through 107 removed outlier: 5.914A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 402 through 412 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 402 through 412 current: chain 'A' and resid 527 through 536 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 527 through 536 current: chain 'A' and resid 569 through 581 Processing sheet with id=AA9, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AB1, first strand: chain 'A' and resid 497 through 504 removed outlier: 5.874A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 625 through 634 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 625 through 634 current: chain 'A' and resid 667 through 674 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 667 through 674 current: chain 'A' and resid 770 through 779 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 642 removed outlier: 3.729A pdb=" N VAL A 656 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB5, first strand: chain 'A' and resid 739 through 744 removed outlier: 11.639A pdb=" N PHE A 739 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N LYS A 756 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 10.421A pdb=" N HIS A 741 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 10.008A pdb=" N LYS A 754 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA A 743 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1558 through 1559 Processing sheet with id=AB7, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB8, first strand: chain 'A' and resid 891 through 901 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 891 through 901 current: chain 'A' and resid 942 through 945 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 942 through 945 current: chain 'A' and resid 1453 through 1463 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1453 through 1463 current: chain 'A' and resid 1495 through 1508 removed outlier: 6.692A pdb=" N GLN A1511 " --> pdb=" O LYS A1507 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.390A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 936 " --> pdb=" O GLU A1446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AC2, first strand: chain 'A' and resid 991 through 995 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1001 through 1012 current: chain 'A' and resid 1080 through 1087 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1093 through 1098 current: chain 'A' and resid 1215 through 1222 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1215 through 1222 current: chain 'A' and resid 1284 through 1288 Processing sheet with id=AC3, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 7.570A pdb=" N GLU A1196 " --> pdb=" O LYS A1189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 457 through 463 removed outlier: 6.604A pdb=" N ILE B 424 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE B 518 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 426 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 570 through 574 removed outlier: 6.555A pdb=" N LEU B 571 " --> pdb=" O TYR B 591 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 590 through 591 current: chain 'B' and resid 627 through 629 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 634 through 636 current: chain 'B' and resid 687 through 691 720 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 8.77 Time building geometry restraints manager: 9.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.34: 6703 1.34 - 1.50: 6402 1.50 - 1.66: 8263 1.66 - 1.82: 130 Bond restraints: 21499 Sorted by residual: bond pdb=" CG PRO A1570 " pdb=" CD PRO A1570 " ideal model delta sigma weight residual 1.503 1.022 0.481 3.40e-02 8.65e+02 2.00e+02 bond pdb=" CA ILE A1519 " pdb=" CB ILE A1519 " ideal model delta sigma weight residual 1.539 1.510 0.029 5.40e-03 3.43e+04 2.82e+01 bond pdb=" N PRO A1570 " pdb=" CD PRO A1570 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" N PRO A1570 " pdb=" CA PRO A1570 " ideal model delta sigma weight residual 1.470 1.513 -0.043 1.22e-02 6.72e+03 1.26e+01 bond pdb=" N VAL A1275 " pdb=" CA VAL A1275 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.07e-02 8.73e+03 4.70e+00 ... (remaining 21494 not shown) Histogram of bond angle deviations from ideal: 77.69 - 89.02: 2 89.02 - 100.34: 16 100.34 - 111.67: 9699 111.67 - 122.99: 17457 122.99 - 134.32: 2109 Bond angle restraints: 29283 Sorted by residual: angle pdb=" N PRO A1570 " pdb=" CD PRO A1570 " pdb=" CG PRO A1570 " ideal model delta sigma weight residual 103.20 77.69 25.51 1.50e+00 4.44e-01 2.89e+02 angle pdb=" CA PRO A1570 " pdb=" CB PRO A1570 " pdb=" CG PRO A1570 " ideal model delta sigma weight residual 104.50 82.22 22.28 1.90e+00 2.77e-01 1.37e+02 angle pdb=" C ASN B 481 " pdb=" N GLU B 482 " pdb=" CA GLU B 482 " ideal model delta sigma weight residual 121.70 134.32 -12.62 1.80e+00 3.09e-01 4.91e+01 angle pdb=" O4' G C 5 " pdb=" C1' G C 5 " pdb=" N9 G C 5 " ideal model delta sigma weight residual 108.20 117.10 -8.90 1.50e+00 4.44e-01 3.52e+01 angle pdb=" N PRO A1570 " pdb=" CA PRO A1570 " pdb=" CB PRO A1570 " ideal model delta sigma weight residual 103.19 97.77 5.42 1.00e+00 1.00e+00 2.94e+01 ... (remaining 29278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.97: 11854 19.97 - 39.95: 760 39.95 - 59.92: 212 59.92 - 79.89: 48 79.89 - 99.86: 19 Dihedral angle restraints: 12893 sinusoidal: 5950 harmonic: 6943 Sorted by residual: dihedral pdb=" CA ASN A 640 " pdb=" C ASN A 640 " pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta harmonic sigma weight residual 180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLN A1059 " pdb=" C GLN A1059 " pdb=" N ASP A1060 " pdb=" CA ASP A1060 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLN A1056 " pdb=" C GLN A1056 " pdb=" N LYS A1057 " pdb=" CA LYS A1057 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 12890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2833 0.083 - 0.165: 273 0.165 - 0.247: 6 0.247 - 0.330: 2 0.330 - 0.412: 1 Chirality restraints: 3115 Sorted by residual: chirality pdb=" C1' G C 5 " pdb=" O4' G C 5 " pdb=" C2' G C 5 " pdb=" N9 G C 5 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C1' U C 11 " pdb=" O4' U C 11 " pdb=" C2' U C 11 " pdb=" N1 U C 11 " both_signs ideal model delta sigma weight residual False 2.45 2.14 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1' A C -2 " pdb=" O4' A C -2 " pdb=" C2' A C -2 " pdb=" N9 A C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 3112 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 876 " -0.414 9.50e-02 1.11e+02 1.86e-01 2.12e+01 pdb=" NE ARG A 876 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 876 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 876 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 876 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 5 " -0.060 2.00e-02 2.50e+03 2.62e-02 2.06e+01 pdb=" N9 G C 5 " 0.064 2.00e-02 2.50e+03 pdb=" C8 G C 5 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G C 5 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G C 5 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G C 5 " -0.014 2.00e-02 2.50e+03 pdb=" N1 G C 5 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G C 5 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G C 5 " 0.009 2.00e-02 2.50e+03 pdb=" N3 G C 5 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G C 5 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 11 " -0.042 2.00e-02 2.50e+03 2.36e-02 1.26e+01 pdb=" N1 U C 11 " 0.056 2.00e-02 2.50e+03 pdb=" C2 U C 11 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U C 11 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U C 11 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U C 11 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U C 11 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U C 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U C 11 " 0.003 2.00e-02 2.50e+03 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 29 2.53 - 3.12: 15080 3.12 - 3.71: 31354 3.71 - 4.31: 47752 4.31 - 4.90: 77329 Nonbonded interactions: 171544 Sorted by model distance: nonbonded pdb=" O ASP A 753 " pdb=" O2' A D -11 " model vdw 1.937 2.440 nonbonded pdb=" O GLU B 482 " pdb=" OG SER B 485 " model vdw 1.959 2.440 nonbonded pdb=" N GLU A 888 " pdb=" OE1 GLU A 888 " model vdw 2.253 2.520 nonbonded pdb=" N GLU A 491 " pdb=" OE1 GLU A 491 " model vdw 2.336 2.520 nonbonded pdb=" NZ LYS A 83 " pdb=" OE1 GLU A 213 " model vdw 2.388 2.520 ... (remaining 171539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.400 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 63.890 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.481 21499 Z= 0.355 Angle : 0.876 25.506 29283 Z= 0.478 Chirality : 0.049 0.412 3115 Planarity : 0.009 0.186 3576 Dihedral : 15.164 99.863 8401 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.82 % Favored : 98.14 % Rotamer: Outliers : 0.14 % Allowed : 10.48 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2365 helix: 0.02 (0.17), residues: 848 sheet: 0.56 (0.24), residues: 428 loop : -0.06 (0.19), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 434 time to evaluate : 2.385 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 435 average time/residue: 1.7592 time to fit residues: 844.8324 Evaluate side-chains 203 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.0170 chunk 184 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 482 ASN A 27 ASN A 43 HIS A 149 HIS A 208 ASN A 464 ASN A 531 GLN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 626 HIS A 640 ASN A 984 GLN A 985 ASN A1001 HIS A1020 HIS A1027 GLN A1168 ASN A1190 ASN A1195 ASN A1246 ASN B 36 GLN B 62 GLN B 716 ASN B 727 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21499 Z= 0.187 Angle : 0.602 10.221 29283 Z= 0.324 Chirality : 0.044 0.343 3115 Planarity : 0.005 0.054 3576 Dihedral : 9.246 99.246 3402 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.31 % Rotamer: Outliers : 2.81 % Allowed : 14.14 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2365 helix: 1.10 (0.18), residues: 833 sheet: 0.70 (0.24), residues: 424 loop : -0.00 (0.19), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 214 time to evaluate : 2.292 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 16 residues processed: 258 average time/residue: 1.7519 time to fit residues: 501.7733 Evaluate side-chains 190 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 2.214 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 1.0758 time to fit residues: 8.1805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 469 HIS A 276 ASN A 464 ASN A 500 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 HIS A 887 HIS A 940 HIS A 984 GLN A1089 ASN A1098 HIS A1190 ASN B 69 GLN B 427 HIS B 632 ASN B 673 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 21499 Z= 0.511 Angle : 0.815 12.749 29283 Z= 0.431 Chirality : 0.055 0.436 3115 Planarity : 0.007 0.136 3576 Dihedral : 9.399 99.497 3402 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 4.14 % Allowed : 14.10 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2365 helix: 0.85 (0.17), residues: 818 sheet: 0.62 (0.24), residues: 446 loop : -0.32 (0.18), residues: 1101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 194 time to evaluate : 2.618 Fit side-chains revert: symmetry clash outliers start: 87 outliers final: 33 residues processed: 262 average time/residue: 1.7871 time to fit residues: 519.0786 Evaluate side-chains 214 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 2.435 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 26 residues processed: 7 average time/residue: 1.1456 time to fit residues: 12.9005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 469 HIS A 113 ASN A 464 ASN A 587 GLN A 626 HIS A1078 ASN A1084 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 362 GLN B 547 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21499 Z= 0.346 Angle : 0.678 11.686 29283 Z= 0.362 Chirality : 0.049 0.407 3115 Planarity : 0.006 0.071 3576 Dihedral : 9.184 98.675 3402 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.24 % Favored : 97.72 % Rotamer: Outliers : 4.05 % Allowed : 15.05 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2365 helix: 1.02 (0.18), residues: 825 sheet: 0.66 (0.24), residues: 431 loop : -0.39 (0.18), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 188 time to evaluate : 2.454 Fit side-chains revert: symmetry clash outliers start: 85 outliers final: 43 residues processed: 254 average time/residue: 1.7737 time to fit residues: 500.7150 Evaluate side-chains 216 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 173 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 5 average time/residue: 0.5190 time to fit residues: 6.9743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A 587 GLN A 626 HIS A1084 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 ASN B 130 HIS B 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21499 Z= 0.367 Angle : 0.696 13.378 29283 Z= 0.368 Chirality : 0.049 0.415 3115 Planarity : 0.006 0.075 3576 Dihedral : 9.232 98.786 3402 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.21 % Rotamer: Outliers : 3.19 % Allowed : 16.48 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2365 helix: 1.04 (0.18), residues: 825 sheet: 0.65 (0.24), residues: 431 loop : -0.47 (0.18), residues: 1109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 182 time to evaluate : 2.482 Fit side-chains outliers start: 67 outliers final: 45 residues processed: 237 average time/residue: 1.7856 time to fit residues: 470.6261 Evaluate side-chains 220 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 175 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 6 average time/residue: 0.4304 time to fit residues: 6.9524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.9990 chunk 211 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A 626 HIS A1084 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1207 ASN A1326 ASN B 256 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21499 Z= 0.191 Angle : 0.559 12.644 29283 Z= 0.299 Chirality : 0.043 0.357 3115 Planarity : 0.005 0.059 3576 Dihedral : 9.166 100.715 3402 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.86 % Favored : 98.10 % Rotamer: Outliers : 3.38 % Allowed : 16.71 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2365 helix: 1.45 (0.18), residues: 825 sheet: 0.75 (0.25), residues: 430 loop : -0.32 (0.18), residues: 1110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 186 time to evaluate : 2.302 Fit side-chains outliers start: 71 outliers final: 40 residues processed: 241 average time/residue: 1.7191 time to fit residues: 462.7777 Evaluate side-chains 214 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 174 time to evaluate : 2.601 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 37 residues processed: 3 average time/residue: 0.8792 time to fit residues: 6.5983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 197 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: