Starting phenix.real_space_refine (version: dev) on Mon May 16 11:09:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr8_21880/05_2022/6wr8_21880_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr8_21880/05_2022/6wr8_21880.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr8_21880/05_2022/6wr8_21880_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr8_21880/05_2022/6wr8_21880_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr8_21880/05_2022/6wr8_21880_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr8_21880/05_2022/6wr8_21880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr8_21880/05_2022/6wr8_21880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr8_21880/05_2022/6wr8_21880_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr8_21880/05_2022/6wr8_21880_trim_updated.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 31608 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': 8, 'TRANS': 220, 'PCIS': 1} 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: {'PTRANS': 55, 'CIS': 3, 'TRANS': 1280, 'PCIS': 1} 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: {'PTRANS': 55, 'CIS': 4, '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: 3836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3836 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 14, 'TRANS': 456} Chain breaks: 2 Chain: "X" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1221 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain breaks: 1 Chain: "Y" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1325 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 2, ' MG': 1} 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 65.362 113.964 82.201 1.00 79.12 S ATOM 14629 SG CYS D 72 65.247 116.223 85.173 1.00 84.70 S ATOM 14737 SG CYS D 85 64.555 117.551 82.112 1.00 83.83 S ATOM 14761 SG CYS D 88 67.815 116.637 82.797 1.00 83.33 S ATOM 20449 SG CYS D 814 101.858 94.979 27.622 1.00 76.02 S ATOM 21014 SG CYS D 888 102.232 95.170 31.388 1.00 64.98 S ATOM 21065 SG CYS D 895 100.779 92.392 29.724 1.00 56.74 S ATOM 21086 SG CYS D 898 104.000 92.656 29.325 1.00 58.54 S Time building chain proxies: 17.33, per 1000 atoms: 0.55 Number of scatterers: 31608 At special positions: 0 Unit cell: (192.24, 189, 156.6, 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 130 16.00 P 124 15.00 Mg 1 11.99 O 6329 8.00 N 5595 7.00 C 19427 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: 14.28 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral 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 895 " 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 888 " Number of angles added : 12 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 38 sheets defined 38.6% alpha, 11.2% beta 49 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 14.73 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.930A 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 161 removed outlier: 4.099A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 232 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 161 removed outlier: 3.706A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 230 removed outlier: 4.750A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (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 206 through 212 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.425A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 328 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: 3.846A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' 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 545 through 548 No H-bonds generated for 'chain 'C' and resid 545 through 548' 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: 3.719A 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 657 through 660 removed outlier: 3.964A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 663 through 667 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: 4.144A 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 820 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 987 through 991 removed outlier: 3.841A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 987 through 991' Processing helix chain 'C' and resid 994 through 997 Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1100 through 1104 Proline residue: C1104 - end of helix 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: 4.904A 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 1242 No H-bonds generated for 'chain 'C' and resid 1239 through 1242' Processing helix chain 'C' and resid 1272 through 1280 Processing helix chain 'C' and resid 1284 through 1291 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 114 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 181 through 190 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 250 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 Processing helix chain 'D' and resid 370 through 387 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 416 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: 3.968A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.526A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 592 Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 614 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 669 Processing helix chain 'D' and resid 675 through 702 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 Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 874 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 925 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1217 through 1224 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.713A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 Processing helix chain 'D' and resid 1280 through 1292 Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1319 through 1325 removed outlier: 4.112A 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 1360 through 1372 removed outlier: 4.349A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 18 through 31 Processing helix chain 'E' and resid 46 through 55 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: 3.790A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 214 through 235 Processing helix chain 'F' and resid 244 through 258 removed outlier: 4.697A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 295 removed outlier: 4.440A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 306 Processing helix chain 'F' and resid 314 through 321 removed outlier: 3.522A pdb=" N ILE F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 351 removed outlier: 4.197A pdb=" N HIS F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 391 removed outlier: 5.380A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 Processing helix chain 'F' and resid 427 through 446 removed outlier: 3.834A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN F 437 " --> pdb=" O TRP F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 Processing helix chain 'F' and resid 480 through 486 Processing helix chain 'F' and resid 492 through 500 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 580 Processing helix chain 'F' and resid 585 through 599 Processing helix chain 'F' and resid 605 through 610 removed outlier: 4.294A pdb=" N PHE F 610 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.314A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 170 through 172 removed outlier: 7.005A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= E, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.960A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 12 through 17 removed outlier: 3.824A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL B 14 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.880A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= I, first strand: chain 'B' and resid 108 through 111 Processing sheet with id= J, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= K, first strand: chain 'C' and resid 143 through 145 Processing sheet with id= L, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= M, first strand: chain 'C' and resid 154 through 158 Processing sheet with id= N, first strand: chain 'C' and resid 227 through 231 Processing sheet with id= O, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= P, first strand: chain 'C' and resid 603 through 606 Processing sheet with id= Q, first strand: chain 'C' and resid 633 through 637 Processing sheet with id= R, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.080A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 1226 through 1232 removed outlier: 4.515A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= U, first strand: chain 'C' and resid 1065 through 1067 Processing sheet with id= V, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.609A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 255 through 257 removed outlier: 5.935A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.321A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.755A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= AA, first strand: chain 'D' and resid 144 through 146 removed outlier: 4.352A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= AC, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= AD, first strand: chain 'D' and resid 547 through 556 Processing sheet with id= AE, first strand: chain 'D' and resid 820 through 823 Processing sheet with id= AF, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.828A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AH, first strand: chain 'D' and resid 1035 through 1038 Processing sheet with id= AI, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 4.248A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 1163 through 1165 removed outlier: 4.395A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 4.401A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 949 through 952 removed outlier: 4.017A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A) 1129 hydrogen bonds defined for protein. 3252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 15.63 Time building geometry restraints manager: 15.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5254 1.30 - 1.43: 8273 1.43 - 1.56: 18328 1.56 - 1.69: 260 1.69 - 1.82: 227 Bond restraints: 32342 Sorted by residual: bond pdb=" C17 1N7 C1402 " pdb=" O3 1N7 C1402 " ideal model delta sigma weight residual 0.000 1.356 -1.356 2.00e-02 2.50e+03 4.60e+03 bond pdb=" C17 1N7 C1401 " pdb=" O3 1N7 C1401 " ideal model delta sigma weight residual 0.000 1.356 -1.356 2.00e-02 2.50e+03 4.60e+03 bond pdb=" C18 1N7 C1402 " pdb=" C6 1N7 C1402 " ideal model delta sigma weight residual 0.987 1.611 -0.624 2.00e-02 2.50e+03 9.72e+02 bond pdb=" C18 1N7 C1401 " pdb=" C6 1N7 C1401 " ideal model delta sigma weight residual 0.987 1.604 -0.617 2.00e-02 2.50e+03 9.52e+02 bond pdb=" C17 1N7 C1402 " pdb=" C18 1N7 C1402 " ideal model delta sigma weight residual 1.147 1.542 -0.395 2.00e-02 2.50e+03 3.90e+02 ... (remaining 32337 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.62: 905 104.62 - 111.97: 16588 111.97 - 119.32: 10879 119.32 - 126.67: 15250 126.67 - 134.03: 598 Bond angle restraints: 44220 Sorted by residual: angle pdb=" C PHE C 15 " pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta sigma weight residual 121.41 109.83 11.58 1.96e+00 2.60e-01 3.49e+01 angle pdb=" C VAL C 550 " pdb=" N HIS C 551 " pdb=" CA HIS C 551 " ideal model delta sigma weight residual 120.97 133.84 -12.87 2.84e+00 1.24e-01 2.05e+01 angle pdb=" C4 1N7 C1401 " pdb=" C5 1N7 C1401 " pdb=" C6 1N7 C1401 " ideal model delta sigma weight residual 112.18 101.15 11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N LEU C1161 " pdb=" CA LEU C1161 " pdb=" C LEU C1161 " ideal model delta sigma weight residual 111.00 121.24 -10.24 2.80e+00 1.28e-01 1.34e+01 angle pdb=" N GLY C 544 " pdb=" CA GLY C 544 " pdb=" C GLY C 544 " ideal model delta sigma weight residual 113.30 103.07 10.23 2.90e+00 1.19e-01 1.24e+01 ... (remaining 44215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 18177 35.26 - 70.52: 1186 70.52 - 105.78: 63 105.78 - 141.04: 3 141.04 - 176.30: 1 Dihedral angle restraints: 19430 sinusoidal: 8812 harmonic: 10618 Sorted by residual: dihedral pdb=" CA LYS C 236 " pdb=" C LYS C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 137.15 42.85 0 5.00e+00 4.00e-02 7.34e+01 dihedral pdb=" CA ASP D1184 " pdb=" C ASP D1184 " pdb=" N PRO D1185 " pdb=" CA PRO D1185 " ideal model delta harmonic sigma weight residual -180.00 -142.36 -37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA THR C 595 " pdb=" C THR C 595 " pdb=" N ASP C 596 " pdb=" CA ASP C 596 " ideal model delta harmonic sigma weight residual 180.00 -142.70 -37.30 0 5.00e+00 4.00e-02 5.57e+01 ... (remaining 19427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.306: 5033 0.306 - 0.612: 4 0.612 - 0.917: 0 0.917 - 1.223: 2 1.223 - 1.529: 2 Chirality restraints: 5041 Sorted by residual: chirality pdb=" C18 1N7 C1402 " pdb=" C17 1N7 C1402 " pdb=" C19 1N7 C1402 " pdb=" C6 1N7 C1402 " both_signs ideal model delta sigma weight residual False 1.21 2.74 -1.53 2.00e-01 2.50e+01 5.84e+01 chirality pdb=" C18 1N7 C1401 " pdb=" C17 1N7 C1401 " pdb=" C19 1N7 C1401 " pdb=" C6 1N7 C1401 " both_signs ideal model delta sigma weight residual False 1.21 2.74 -1.52 2.00e-01 2.50e+01 5.78e+01 chirality pdb=" C6 1N7 C1402 " pdb=" C18 1N7 C1402 " pdb=" C5 1N7 C1402 " pdb=" C7 1N7 C1402 " both_signs ideal model delta sigma weight residual False -1.78 -2.84 1.06 2.00e-01 2.50e+01 2.82e+01 ... (remaining 5038 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C1223 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO C1224 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO C1224 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C1224 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 426 " 0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO D 427 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG Y 21 " -0.025 2.00e-02 2.50e+03 1.45e-02 6.29e+00 pdb=" N9 DG Y 21 " 0.040 2.00e-02 2.50e+03 pdb=" C8 DG Y 21 " -0.013 2.00e-02 2.50e+03 pdb=" N7 DG Y 21 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG Y 21 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG Y 21 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG Y 21 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG Y 21 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG Y 21 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG Y 21 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG Y 21 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG Y 21 " 0.004 2.00e-02 2.50e+03 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 300 2.43 - 3.05: 23984 3.05 - 3.66: 48896 3.66 - 4.28: 71728 4.28 - 4.90: 115875 Nonbonded interactions: 260783 Sorted by model distance: nonbonded pdb=" OD1 ASP C 826 " pdb=" OG1 THR C 829 " model vdw 1.812 2.440 nonbonded pdb=" OD1 ASN D 768 " pdb=" NE2 GLN D 771 " model vdw 1.847 2.520 nonbonded pdb=" O LEU D1344 " pdb=" N GLY D1346 " model vdw 1.886 2.520 nonbonded pdb=" OG1 THR D 980 " pdb=" O VAL D 997 " model vdw 1.887 2.440 nonbonded pdb=" O LYS D 964 " pdb=" OG1 THR D 976 " model vdw 1.931 2.440 ... (remaining 260778 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 124 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19427 2.51 5 N 5595 2.21 5 O 6329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 13.770 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.300 Process input model: 98.920 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.016 1.356 32342 Z= 0.889 Angle : 0.910 17.689 44220 Z= 0.502 Chirality : 0.062 1.529 5041 Planarity : 0.005 0.091 5331 Dihedral : 20.296 176.296 12586 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 56.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.02 % Favored : 91.38 % Rotamer Outliers : 7.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.12), residues: 3668 helix: -1.00 (0.11), residues: 1479 sheet: -0.89 (0.23), residues: 400 loop : -2.85 (0.12), residues: 1789 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 206 time to evaluate : 3.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 248 outliers final: 179 residues processed: 444 average time/residue: 0.4249 time to fit residues: 305.2617 Evaluate side-chains 355 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 176 time to evaluate : 3.640 Switching outliers to nearest non-outliers outliers start: 179 outliers final: 0 residues processed: 179 average time/residue: 0.3278 time to fit residues: 108.7729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 1.9990 chunk 288 optimal weight: 30.0000 chunk 159 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 297 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 345 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS B 127 GLN B 132 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 437 ASN C 554 HIS C 659 GLN C1017 GLN C1209 GLN C1236 ASN C1288 GLN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1114 GLN D1279 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.114 32342 Z= 0.267 Angle : 0.784 13.829 44220 Z= 0.400 Chirality : 0.046 0.278 5041 Planarity : 0.005 0.076 5331 Dihedral : 18.924 174.638 5298 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.22 % Favored : 93.65 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 3668 helix: 0.43 (0.13), residues: 1459 sheet: -0.60 (0.24), residues: 419 loop : -2.20 (0.13), residues: 1790 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 212 time to evaluate : 3.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 28 residues processed: 268 average time/residue: 0.4179 time to fit residues: 186.3232 Evaluate side-chains 200 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 4.328 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3461 time to fit residues: 23.4965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 287 optimal weight: 0.4980 chunk 234 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 373 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 342 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 277 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.109 32342 Z= 0.269 Angle : 0.805 25.531 44220 Z= 0.404 Chirality : 0.045 0.275 5041 Planarity : 0.005 0.076 5331 Dihedral : 18.924 174.640 5298 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.22 % Favored : 93.65 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3668 helix: 0.44 (0.13), residues: 1459 sheet: -0.60 (0.24), residues: 419 loop : -2.20 (0.13), residues: 1790 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.4363 time to fit residues: 126.3940 Evaluate side-chains 171 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 3.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 0.9990 chunk 259 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 346 optimal weight: 7.9990 chunk 367 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 328 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 573 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 32342 Z= 0.358 Angle : 0.747 15.083 44220 Z= 0.383 Chirality : 0.044 0.220 5041 Planarity : 0.005 0.070 5331 Dihedral : 18.831 172.757 5298 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 3668 helix: 0.73 (0.13), residues: 1467 sheet: -0.36 (0.25), residues: 408 loop : -2.01 (0.13), residues: 1793 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 184 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 26 residues processed: 228 average time/residue: 0.4366 time to fit residues: 166.2387 Evaluate side-chains 198 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 3.842 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3675 time to fit residues: 21.7144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 273 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 329 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 32342 Z= 0.414 Angle : 0.762 16.768 44220 Z= 0.386 Chirality : 0.044 0.221 5041 Planarity : 0.005 0.069 5331 Dihedral : 18.828 172.777 5298 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.21 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.11 % 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: -0.98 (0.13), residues: 3668 helix: 0.75 (0.13), residues: 1467 sheet: -0.34 (0.25), residues: 408 loop : -1.99 (0.13), residues: 1793 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 28 residues processed: 201 average time/residue: 0.4264 time to fit residues: 143.5615 Evaluate side-chains 201 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 3.866 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3119 time to fit residues: 20.9321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 367 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 32342 Z= 0.414 Angle : 0.762 16.768 44220 Z= 0.386 Chirality : 0.044 0.221 5041 Planarity : 0.005 0.069 5331 Dihedral : 18.828 172.777 5298 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.11 % 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: -0.98 (0.13), residues: 3668 helix: 0.75 (0.13), residues: 1467 sheet: -0.34 (0.25), residues: 408 loop : -1.99 (0.13), residues: 1793 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.4399 time to fit residues: 127.0505 Evaluate side-chains 171 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 4.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 366 optimal weight: 20.0000 chunk 229 optimal weight: 0.5980 chunk 223 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 32342 Z= 0.413 Angle : 0.762 16.756 44220 Z= 0.386 Chirality : 0.044 0.220 5041 Planarity : 0.005 0.069 5331 Dihedral : 18.828 172.777 5298 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.21 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.11 % 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: -0.98 (0.13), residues: 3668 helix: 0.75 (0.13), residues: 1467 sheet: -0.34 (0.25), residues: 408 loop : -1.99 (0.13), residues: 1793 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 172 average time/residue: 0.4356 time to fit residues: 125.5026 Evaluate side-chains 173 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 3.789 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2759 time to fit residues: 5.4937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 218 optimal weight: 0.0270 chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 0.0000 chunk 232 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 overall best weight: 0.9846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 32342 Z= 0.270 Angle : 0.740 15.359 44220 Z= 0.376 Chirality : 0.044 0.248 5041 Planarity : 0.005 0.066 5331 Dihedral : 18.829 172.753 5298 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.11 % 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: -0.91 (0.13), residues: 3668 helix: 0.81 (0.13), residues: 1467 sheet: -0.36 (0.25), residues: 421 loop : -1.94 (0.13), residues: 1780 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 191 average time/residue: 0.4501 time to fit residues: 142.5013 Evaluate side-chains 179 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 3.697 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3005 time to fit residues: 8.3073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 6.9990 chunk 350 optimal weight: 9.9990 chunk 320 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 chunk 340 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 32342 Z= 0.270 Angle : 0.740 15.359 44220 Z= 0.376 Chirality : 0.044 0.248 5041 Planarity : 0.005 0.066 5331 Dihedral : 18.829 172.753 5298 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.11 % 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: -0.91 (0.13), residues: 3668 helix: 0.81 (0.13), residues: 1467 sheet: -0.36 (0.25), residues: 421 loop : -1.94 (0.13), residues: 1780 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 3.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.4401 time to fit residues: 127.7234 Evaluate side-chains 174 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.786 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 0.6980 chunk 360 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 250 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 32342 Z= 0.270 Angle : 0.741 15.359 44220 Z= 0.376 Chirality : 0.043 0.248 5041 Planarity : 0.005 0.066 5331 Dihedral : 18.829 172.753 5298 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.11 % 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: -0.91 (0.13), residues: 3668 helix: 0.81 (0.13), residues: 1467 sheet: -0.36 (0.25), residues: 421 loop : -1.94 (0.13), residues: 1780 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.4360 time to fit residues: 126.4623 Evaluate side-chains 173 residues out of total 3157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 4.9990 chunk 321 optimal weight: 0.0000 chunk 92 optimal weight: 4.9990 chunk 277 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.101395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.068740 restraints weight = 107416.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068827 restraints weight = 72101.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.069244 restraints weight = 49593.953| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 32342 Z= 0.270 Angle : 0.741 15.359 44220 Z= 0.376 Chirality : 0.043 0.248 5041 Planarity : 0.005 0.066 5331 Dihedral : 18.829 172.753 5298 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.20 % Twisted Proline : 0.69 % Twisted General : 0.11 % 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: -0.91 (0.13), residues: 3668 helix: 0.81 (0.13), residues: 1467 sheet: -0.36 (0.25), residues: 421 loop : -1.94 (0.13), residues: 1780 =============================================================================== Job complete usr+sys time: 4807.75 seconds wall clock time: 89 minutes 45.36 seconds (5385.36 seconds total)