Starting phenix.real_space_refine (version: dev) on Mon Feb 27 14:35:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/02_2023/6n57_0348_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/02_2023/6n57_0348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/02_2023/6n57_0348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/02_2023/6n57_0348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/02_2023/6n57_0348_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n57_0348/02_2023/6n57_0348_trim_updated.pdb" } resolution = 3.7 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 30233 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1347, 10479 Classifications: {'peptide': 1347} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1290} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 4423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4423 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 2, 'PTRANS': 16, 'TRANS': 536} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "M" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20313 SG CYS J 814 25.504 89.870 82.477 1.00 34.14 S ATOM 20878 SG CYS J 888 28.493 88.510 84.421 1.00 38.06 S ATOM 20929 SG CYS J 895 27.462 87.320 81.418 1.00 21.90 S ATOM 20950 SG CYS J 898 28.060 90.381 80.150 1.00 24.08 S ATOM 14479 SG CYS J 70 50.502 39.237 119.673 1.00 46.89 S ATOM 14493 SG CYS J 72 52.431 37.499 122.064 1.00 47.01 S ATOM 14601 SG CYS J 85 48.798 37.822 122.466 1.00 68.08 S ATOM 14625 SG CYS J 88 51.793 41.223 122.111 1.00 58.98 S ATOM 29831 SG CYS M 37 76.970 129.893 81.580 1.00 66.53 S ATOM 29851 SG CYS M 40 79.508 131.735 83.020 1.00 64.05 S ATOM 29988 SG CYS M 58 80.825 128.222 80.883 1.00 49.44 S Time building chain proxies: 16.69, per 1000 atoms: 0.55 Number of scatterers: 30233 At special positions: 0 Unit cell: (153.4, 163.8, 193.7, 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 3 29.99 S 136 16.00 Mg 1 11.99 O 5805 8.00 N 5327 7.00 C 18961 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.72 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 814 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 72 " pdb=" ZN M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 58 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 40 " Number of angles added : 12 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 31 sheets defined 36.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 87 removed outlier: 4.286A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 230 removed outlier: 4.730A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 87 Processing helix chain 'I' and resid 206 through 212 removed outlier: 3.515A pdb=" N ILE I 209 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 223 Processing helix chain 'I' and resid 271 through 278 Processing helix chain 'I' and resid 289 through 292 No H-bonds generated for 'chain 'I' and resid 289 through 292' Processing helix chain 'I' and resid 319 through 326 Processing helix chain 'I' and resid 347 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 388 Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.984A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 526 Processing helix chain 'I' and resid 545 through 547 No H-bonds generated for 'chain 'I' and resid 545 through 547' Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 removed outlier: 4.675A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 980 removed outlier: 3.844A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1100 through 1102 No H-bonds generated for 'chain 'I' and resid 1100 through 1102' Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1150 Processing helix chain 'I' and resid 1166 through 1176 removed outlier: 4.400A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1242 No H-bonds generated for 'chain 'I' and resid 1239 through 1242' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1300 through 1309 Processing helix chain 'I' and resid 1322 through 1332 Processing helix chain 'J' and resid 27 through 32 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 96 through 99 Processing helix chain 'J' and resid 115 through 118 No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 125 through 128 No H-bonds generated for 'chain 'J' and resid 125 through 128' Processing helix chain 'J' and resid 132 through 140 Processing helix chain 'J' and resid 162 through 171 removed outlier: 3.562A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 191 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 removed outlier: 3.905A pdb=" N MET J 237 " --> pdb=" O PRO J 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 234 through 237' Processing helix chain 'J' and resid 265 through 285 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 337 through 341 Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 3.963A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 457 Processing helix chain 'J' and resid 475 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 539 removed outlier: 3.619A pdb=" N SER J 539 " --> pdb=" O ARG J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 598 through 612 removed outlier: 3.897A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 634 Processing helix chain 'J' and resid 650 through 668 removed outlier: 3.744A pdb=" N ALA J 662 " --> pdb=" O GLU J 658 " (cutoff:3.500A) Processing helix chain 'J' and resid 675 through 701 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 769 through 786 removed outlier: 3.836A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 788 through 791 No H-bonds generated for 'chain 'J' and resid 788 through 791' Processing helix chain 'J' and resid 795 through 803 removed outlier: 3.638A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 866 through 874 Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 915 through 929 Proline residue: J 926 - end of helix removed outlier: 4.286A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1139 through 1146 Processing helix chain 'J' and resid 1217 through 1223 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 4.196A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1262 removed outlier: 4.301A pdb=" N ARG J1262 " --> pdb=" O ARG J1258 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1312 No H-bonds generated for 'chain 'J' and resid 1309 through 1312' Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 3.641A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 79 removed outlier: 3.603A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 19 Processing helix chain 'L' and resid 24 through 30 Processing helix chain 'L' and resid 40 through 50 Processing helix chain 'L' and resid 77 through 89 Processing helix chain 'L' and resid 98 through 105 Processing helix chain 'L' and resid 116 through 136 Processing helix chain 'L' and resid 138 through 153 Processing helix chain 'L' and resid 158 through 161 No H-bonds generated for 'chain 'L' and resid 158 through 161' Processing helix chain 'L' and resid 214 through 232 Processing helix chain 'L' and resid 245 through 256 Processing helix chain 'L' and resid 263 through 295 removed outlier: 4.003A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU L 293 " --> pdb=" O LYS L 289 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN L 294 " --> pdb=" O LEU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 306 removed outlier: 4.815A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 321 removed outlier: 4.266A pdb=" N ALA L 319 " --> pdb=" O TRP L 315 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA L 321 " --> pdb=" O ASN L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 351 Processing helix chain 'L' and resid 355 through 394 removed outlier: 4.872A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS L 393 " --> pdb=" O SER L 389 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 445 removed outlier: 3.856A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 473 Processing helix chain 'L' and resid 480 through 486 removed outlier: 4.069A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 519 through 522 Processing helix chain 'L' and resid 531 through 549 Processing helix chain 'L' and resid 553 through 561 Processing helix chain 'L' and resid 573 through 580 Processing helix chain 'L' and resid 585 through 599 Processing helix chain 'L' and resid 605 through 610 Processing helix chain 'M' and resid 6 through 26 Processing helix chain 'M' and resid 46 through 51 Processing helix chain 'M' and resid 59 through 71 removed outlier: 4.187A pdb=" N HIS M 71 " --> pdb=" O ARG M 67 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 23 through 27 Processing sheet with id= B, first strand: chain 'G' and resid 102 through 105 Processing sheet with id= C, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.500A pdb=" N GLY G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 187 through 190 Processing sheet with id= E, first strand: chain 'H' and resid 53 through 61 removed outlier: 3.753A pdb=" N GLY H 53 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY H 149 " --> pdb=" O GLY H 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 67 through 69 removed outlier: 3.769A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 73 through 75 Processing sheet with id= H, first strand: chain 'I' and resid 155 through 157 Processing sheet with id= I, first strand: chain 'I' and resid 184 through 188 Processing sheet with id= J, first strand: chain 'I' and resid 227 through 230 Processing sheet with id= K, first strand: chain 'I' and resid 591 through 593 Processing sheet with id= L, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= M, first strand: chain 'I' and resid 798 through 802 removed outlier: 3.623A pdb=" N GLN I 798 " --> pdb=" O MET I1232 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 830 through 833 Processing sheet with id= O, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= P, first strand: chain 'I' and resid 930 through 933 removed outlier: 3.909A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 255 through 257 removed outlier: 3.530A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 722 through 727 removed outlier: 6.544A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.727A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 252 through 254 removed outlier: 4.169A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 365 through 369 removed outlier: 5.696A pdb=" N GLU J 438 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU J 368 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL J 440 " --> pdb=" O LEU J 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'J' and resid 434 through 437 removed outlier: 3.513A pdb=" N GLN J 435 " --> pdb=" O LEU J 423 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 553 through 556 removed outlier: 3.891A pdb=" N GLU J 554 " --> pdb=" O LYS J 566 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS J 566 " --> pdb=" O GLU J 554 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU J 556 " --> pdb=" O VAL J 564 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 820 through 823 removed outlier: 3.635A pdb=" N MET J 822 " --> pdb=" O VAL J 880 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.573A pdb=" N LYS J 959 " --> pdb=" O LYS J 983 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.379A pdb=" N VAL J 974 " --> pdb=" O VAL J 966 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 1046 through 1049 Processing sheet with id= AB, first strand: chain 'J' and resid 1077 through 1079 Processing sheet with id= AC, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AD, first strand: chain 'J' and resid 1279 through 1281 Processing sheet with id= AE, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.025A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.15 Time building geometry restraints manager: 13.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10356 1.34 - 1.46: 6246 1.46 - 1.59: 13818 1.59 - 1.72: 14 1.72 - 1.84: 245 Bond restraints: 30679 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.841 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C19 1N7 M 102 " pdb=" C3 1N7 M 102 " ideal model delta sigma weight residual 1.532 1.815 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.738 -0.206 2.00e-02 2.50e+03 1.07e+02 ... (remaining 30674 not shown) Histogram of bond angle deviations from ideal: 90.84 - 100.88: 85 100.88 - 110.91: 11632 110.91 - 120.94: 21186 120.94 - 130.98: 8471 130.98 - 141.01: 73 Bond angle restraints: 41447 Sorted by residual: angle pdb=" N GLU L 58 " pdb=" CA GLU L 58 " pdb=" CB GLU L 58 " ideal model delta sigma weight residual 110.49 141.01 -30.52 1.69e+00 3.50e-01 3.26e+02 angle pdb=" C PHE J 437 " pdb=" N GLU J 438 " pdb=" CA GLU J 438 " ideal model delta sigma weight residual 121.92 104.59 17.33 1.60e+00 3.91e-01 1.17e+02 angle pdb=" N GLU L 58 " pdb=" CA GLU L 58 " pdb=" C GLU L 58 " ideal model delta sigma weight residual 110.80 90.84 19.96 2.13e+00 2.20e-01 8.78e+01 angle pdb=" C GLU H 29 " pdb=" N PRO H 30 " pdb=" CD PRO H 30 " ideal model delta sigma weight residual 120.60 136.83 -16.23 2.20e+00 2.07e-01 5.44e+01 angle pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CD PRO I 58 " ideal model delta sigma weight residual 120.60 136.16 -15.56 2.20e+00 2.07e-01 5.00e+01 ... (remaining 41442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 18215 19.50 - 39.00: 619 39.00 - 58.50: 45 58.50 - 78.00: 26 78.00 - 97.50: 2 Dihedral angle restraints: 18907 sinusoidal: 7838 harmonic: 11069 Sorted by residual: dihedral pdb=" N GLU L 58 " pdb=" C GLU L 58 " pdb=" CA GLU L 58 " pdb=" CB GLU L 58 " ideal model delta harmonic sigma weight residual 122.80 146.50 -23.70 0 2.50e+00 1.60e-01 8.99e+01 dihedral pdb=" CA THR J 853 " pdb=" C THR J 853 " pdb=" N ALA J 854 " pdb=" CA ALA J 854 " ideal model delta harmonic sigma weight residual 180.00 135.88 44.12 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA PRO I 897 " pdb=" C PRO I 897 " pdb=" N GLU I 898 " pdb=" CA GLU I 898 " ideal model delta harmonic sigma weight residual -180.00 -139.53 -40.47 0 5.00e+00 4.00e-02 6.55e+01 ... (remaining 18904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4683 0.149 - 0.298: 63 0.298 - 0.448: 3 0.448 - 0.597: 1 0.597 - 0.746: 1 Chirality restraints: 4751 Sorted by residual: chirality pdb=" CA GLU L 58 " pdb=" N GLU L 58 " pdb=" C GLU L 58 " pdb=" CB GLU L 58 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA GLU G 29 " pdb=" N GLU G 29 " pdb=" C GLU G 29 " pdb=" CB GLU G 29 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 4748 not shown) Planarity restraints: 5415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 96 " -0.124 5.00e-02 4.00e+02 2.00e-01 6.43e+01 pdb=" N PRO L 97 " 0.347 5.00e-02 4.00e+02 pdb=" CA PRO L 97 " -0.125 5.00e-02 4.00e+02 pdb=" CD PRO L 97 " -0.098 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 59 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO L 60 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 438 " 0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO J 439 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO J 439 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO J 439 " 0.048 5.00e-02 4.00e+02 ... (remaining 5412 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 15 2.07 - 2.78: 7389 2.78 - 3.49: 43518 3.49 - 4.19: 68374 4.19 - 4.90: 120685 Nonbonded interactions: 239981 Sorted by model distance: nonbonded pdb=" NH1 ARG J 933 " pdb=" OD2 ASP L 63 " model vdw 1.366 2.520 nonbonded pdb=" O ASP L 63 " pdb=" N LEU L 65 " model vdw 1.570 2.520 nonbonded pdb=" OH TYR L 148 " pdb=" OE2 GLU L 152 " model vdw 1.824 2.440 nonbonded pdb=" O THR I 539 " pdb=" O ALA I 543 " model vdw 1.884 3.040 nonbonded pdb=" OD1 ASP L 96 " pdb=" N PRO L 97 " model vdw 1.956 3.120 ... (remaining 239976 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 'G' and (resid 8 through 158 or resid 171 through 233 or (resid 234 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 8 through 228 or (resid 229 through 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 234)) } 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 Mg 1 5.21 5 S 136 5.16 5 C 18961 2.51 5 N 5327 2.21 5 O 5805 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 6.800 Check model and map are aligned: 0.490 Process input model: 82.810 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.290 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.012 0.309 30679 Z= 0.800 Angle : 1.135 30.518 41447 Z= 0.609 Chirality : 0.060 0.746 4751 Planarity : 0.007 0.200 5415 Dihedral : 10.412 97.497 11769 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 39.05 Ramachandran Plot: Outliers : 0.60 % Allowed : 15.43 % Favored : 83.97 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.67 % Twisted General : 0.22 % 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: -4.55 (0.11), residues: 3817 helix: -2.11 (0.11), residues: 1526 sheet: -3.68 (0.23), residues: 349 loop : -3.76 (0.12), residues: 1942 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 801 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 810 average time/residue: 0.4967 time to fit residues: 604.2851 Evaluate side-chains 417 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 414 time to evaluate : 3.930 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2675 time to fit residues: 7.2766 ------------------------------------------------------------------------------- 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: 0.0770 chunk 288 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 297 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 345 optimal weight: 7.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS G 147 GLN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 133 ASN I 219 GLN I 343 HIS I 510 GLN I 620 ASN I 808 ASN I1017 GLN I1080 ASN I1116 HIS I1209 GLN I1257 GLN J 232 ASN J 341 ASN J 680 ASN J 720 ASN J 910 ASN J1197 ASN J1268 ASN J1295 ASN J1366 HIS K 70 GLN L 40 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 346 GLN L 383 ASN L 406 GLN L 518 HIS L 568 ASN M 21 ASN ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 30679 Z= 0.204 Angle : 0.711 19.211 41447 Z= 0.356 Chirality : 0.045 0.393 4751 Planarity : 0.006 0.129 5415 Dihedral : 5.868 70.230 4222 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.20 % Favored : 92.48 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.99 (0.12), residues: 3817 helix: -0.45 (0.13), residues: 1502 sheet: -3.29 (0.23), residues: 355 loop : -3.07 (0.12), residues: 1960 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 612 time to evaluate : 4.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 33 residues processed: 666 average time/residue: 0.4627 time to fit residues: 486.9800 Evaluate side-chains 428 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 395 time to evaluate : 4.010 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3089 time to fit residues: 24.6465 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 4.9990 chunk 287 optimal weight: 0.4980 chunk 234 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 345 optimal weight: 8.9990 chunk 373 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 chunk 342 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 132 HIS I 613 ASN I 620 ASN ** I 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1314 GLN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1350 ASN L 129 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 30679 Z= 0.340 Angle : 0.718 19.026 41447 Z= 0.357 Chirality : 0.046 0.300 4751 Planarity : 0.005 0.099 5415 Dihedral : 5.642 43.514 4222 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.51 % Favored : 90.23 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.51 (0.13), residues: 3817 helix: -0.05 (0.13), residues: 1510 sheet: -2.88 (0.26), residues: 319 loop : -2.87 (0.12), residues: 1988 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 436 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 57 residues processed: 510 average time/residue: 0.4354 time to fit residues: 357.9447 Evaluate side-chains 427 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 370 time to evaluate : 3.721 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.2881 time to fit residues: 36.0031 ------------------------------------------------------------------------------- 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: 5.9990 chunk 259 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 346 optimal weight: 20.0000 chunk 367 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 328 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I 613 ASN I 684 ASN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 30679 Z= 0.252 Angle : 0.659 18.986 41447 Z= 0.327 Chirality : 0.044 0.208 4751 Planarity : 0.005 0.069 5415 Dihedral : 5.293 42.903 4222 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.12 % Favored : 91.62 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % 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: -2.11 (0.13), residues: 3817 helix: 0.26 (0.13), residues: 1519 sheet: -2.52 (0.27), residues: 329 loop : -2.66 (0.13), residues: 1969 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 430 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 28 residues processed: 476 average time/residue: 0.4893 time to fit residues: 380.5947 Evaluate side-chains 393 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 365 time to evaluate : 3.877 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3155 time to fit residues: 22.0757 ------------------------------------------------------------------------------- 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: 8.9990 chunk 208 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 273 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 313 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 329 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN I 69 GLN I 613 ASN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN J 979 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN L 437 GLN L 568 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 30679 Z= 0.383 Angle : 0.714 18.186 41447 Z= 0.356 Chirality : 0.046 0.215 4751 Planarity : 0.005 0.064 5415 Dihedral : 5.457 42.479 4222 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.80 % Favored : 89.97 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % 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: -2.04 (0.13), residues: 3817 helix: 0.30 (0.13), residues: 1520 sheet: -2.53 (0.28), residues: 309 loop : -2.60 (0.13), residues: 1988 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 390 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 46 residues processed: 447 average time/residue: 0.4345 time to fit residues: 311.1092 Evaluate side-chains 416 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 370 time to evaluate : 3.964 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2807 time to fit residues: 30.1057 ------------------------------------------------------------------------------- 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: 1.9990 chunk 330 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 90 optimal weight: 0.0770 chunk 367 optimal weight: 8.9990 chunk 305 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 580 GLN I 613 ASN J 294 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 30679 Z= 0.186 Angle : 0.616 17.761 41447 Z= 0.305 Chirality : 0.043 0.224 4751 Planarity : 0.004 0.063 5415 Dihedral : 5.002 42.957 4222 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.31 % Favored : 92.51 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % 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: -1.65 (0.13), residues: 3817 helix: 0.64 (0.14), residues: 1523 sheet: -1.98 (0.28), residues: 328 loop : -2.46 (0.13), residues: 1966 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 412 time to evaluate : 4.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 23 residues processed: 441 average time/residue: 0.4465 time to fit residues: 316.6103 Evaluate side-chains 385 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 362 time to evaluate : 3.797 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3034 time to fit residues: 18.6415 ------------------------------------------------------------------------------- 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: 9.9990 chunk 41 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 268 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 309 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 366 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 613 ASN I1017 GLN I1257 GLN J 294 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN M 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 30679 Z= 0.181 Angle : 0.608 17.051 41447 Z= 0.299 Chirality : 0.042 0.240 4751 Planarity : 0.004 0.063 5415 Dihedral : 4.757 42.518 4222 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.60 % Favored : 92.19 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 3817 helix: 0.87 (0.14), residues: 1520 sheet: -1.66 (0.29), residues: 318 loop : -2.33 (0.13), residues: 1979 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 404 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 424 average time/residue: 0.4687 time to fit residues: 316.1453 Evaluate side-chains 387 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 367 time to evaluate : 3.751 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2738 time to fit residues: 15.6419 ------------------------------------------------------------------------------- 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: 3.9990 chunk 146 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 232 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 314 ASN I 613 ASN ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN J 907 HIS L 49 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30679 Z= 0.226 Angle : 0.620 15.031 41447 Z= 0.307 Chirality : 0.043 0.246 4751 Planarity : 0.004 0.061 5415 Dihedral : 4.773 42.007 4222 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.07 % Favored : 91.72 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.27 (0.14), residues: 3817 helix: 0.91 (0.14), residues: 1522 sheet: -1.51 (0.29), residues: 324 loop : -2.26 (0.13), residues: 1971 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 377 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 394 average time/residue: 0.4615 time to fit residues: 293.5204 Evaluate side-chains 379 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 360 time to evaluate : 3.822 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3176 time to fit residues: 15.8792 ------------------------------------------------------------------------------- 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: 0.0060 chunk 350 optimal weight: 6.9990 chunk 320 optimal weight: 9.9990 chunk 341 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 340 optimal weight: 7.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 30679 Z= 0.283 Angle : 0.657 13.944 41447 Z= 0.323 Chirality : 0.044 0.273 4751 Planarity : 0.004 0.060 5415 Dihedral : 4.900 41.773 4222 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.72 % Favored : 91.07 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.29 (0.14), residues: 3817 helix: 0.85 (0.13), residues: 1523 sheet: -1.48 (0.29), residues: 325 loop : -2.23 (0.13), residues: 1969 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 366 time to evaluate : 4.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 379 average time/residue: 0.4575 time to fit residues: 277.6428 Evaluate side-chains 370 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 350 time to evaluate : 3.793 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2818 time to fit residues: 16.0043 ------------------------------------------------------------------------------- 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: 0.7980 chunk 360 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 378 optimal weight: 0.5980 chunk 348 optimal weight: 20.0000 chunk 301 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN L 49 ASN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 30679 Z= 0.271 Angle : 0.656 14.531 41447 Z= 0.324 Chirality : 0.044 0.359 4751 Planarity : 0.004 0.061 5415 Dihedral : 4.904 41.956 4222 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.51 % Favored : 91.28 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.28 (0.14), residues: 3817 helix: 0.82 (0.13), residues: 1528 sheet: -1.44 (0.29), residues: 325 loop : -2.21 (0.13), residues: 1964 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 363 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 365 average time/residue: 0.4802 time to fit residues: 280.0629 Evaluate side-chains 359 residues out of total 3287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 352 time to evaluate : 3.897 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2943 time to fit residues: 8.8974 ------------------------------------------------------------------------------- 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: 2.9990 chunk 321 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 277 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 55 optimal weight: 0.0970 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 GLN J 294 ASN J1023 HIS J1244 GLN ** L 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116033 restraints weight = 45091.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113953 restraints weight = 69016.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115637 restraints weight = 63099.253| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 30679 Z= 0.189 Angle : 0.616 14.140 41447 Z= 0.303 Chirality : 0.043 0.385 4751 Planarity : 0.004 0.061 5415 Dihedral : 4.684 42.065 4222 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.47 % Favored : 92.32 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.11 (0.14), residues: 3817 helix: 1.00 (0.13), residues: 1515 sheet: -1.28 (0.30), residues: 319 loop : -2.13 (0.13), residues: 1983 =============================================================================== Job complete usr+sys time: 6717.26 seconds wall clock time: 123 minutes 17.39 seconds (7397.39 seconds total)