Starting phenix.real_space_refine (version: dev) on Mon May 16 14:55:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrg_21883/05_2022/6wrg_21883_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrg_21883/05_2022/6wrg_21883.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrg_21883/05_2022/6wrg_21883_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrg_21883/05_2022/6wrg_21883_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrg_21883/05_2022/6wrg_21883_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrg_21883/05_2022/6wrg_21883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrg_21883/05_2022/6wrg_21883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrg_21883/05_2022/6wrg_21883_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrg_21883/05_2022/6wrg_21883_trim_updated.pdb" } resolution = 3.58 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= 0.033 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 Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 32527 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 8, 'TRANS': 218, 'PCIS': 1} Chain: "C" Number of atoms: 10564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10564 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'CIS': 2, 'TRANS': 1281, 'PCIS': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 10516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1363, 10516 Classifications: {'peptide': 1363} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 55, 'CIS': 7, 'TRANS': 1300} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 36 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: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1101 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Chain: "Y" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 951 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "M" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 136} 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: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Unusual residues: {'G4P': 1, ' ZN': 2, ' MG': 1, '1N7': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'G4P': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14583 SG CYS D 70 49.040 117.961 70.237 1.00107.20 S ATOM 14597 SG CYS D 72 50.602 118.173 67.072 1.00108.13 S ATOM 14705 SG CYS D 85 47.394 117.288 67.284 1.00106.91 S ATOM 14729 SG CYS D 88 49.834 115.060 68.304 1.00102.07 S ATOM 20393 SG CYS D 814 27.387 70.578 114.480 1.00 84.18 S ATOM 20958 SG CYS D 888 30.484 71.283 113.238 1.00 79.39 S ATOM 21009 SG CYS D 895 29.045 73.048 115.823 1.00 77.26 S ATOM 21030 SG CYS D 898 30.001 70.237 116.310 1.00 76.36 S ATOM 31998 SG CYS M 114 84.687 34.451 120.104 1.00118.39 S ATOM 32019 SG CYS M 117 87.449 32.038 119.635 1.00122.05 S ATOM 32155 SG CYS M 135 88.060 35.189 121.481 1.00115.65 S ATOM 32177 SG CYS M 138 87.833 35.275 118.022 1.00116.57 S Time building chain proxies: 18.55, per 1000 atoms: 0.57 Number of scatterers: 32527 At special positions: 0 Unit cell: (150.12, 173.88, 197.64, 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 3 29.99 S 140 16.00 P 108 15.00 Mg 1 11.99 O 6488 8.00 N 5743 7.00 C 20044 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.79 Conformation dependent library (CDL) restraints added in 4.5 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 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 135 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 138 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 117 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 114 " Number of angles added : 18 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 131 helices and 34 sheets defined 38.9% alpha, 10.5% beta 45 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 13.19 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.036A 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 157 through 161 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 160 Processing helix chain 'B' and resid 213 through 230 removed outlier: 4.766A 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 38 Processing helix chain 'C' and resid 50 through 56 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 319 through 328 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 360 through 370 removed outlier: 4.739A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 456 through 481 Processing helix chain 'C' and resid 495 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 608 through 613 removed outlier: 4.043A 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: 3.950A 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: 4.025A 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 864 removed outlier: 4.766A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 979 Processing helix chain 'C' and resid 987 through 991 Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1082 through 1084 No H-bonds generated for 'chain 'C' and resid 1082 through 1084' Processing helix chain 'C' and resid 1100 through 1105 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: 5.005A 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 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 264 through 284 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 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 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: 3.848A 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 580 Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 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 804 removed outlier: 4.101A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 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 1138 through 1146 Processing helix chain 'D' and resid 1217 through 1224 Processing helix chain 'D' and resid 1226 through 1243 removed outlier: 3.659A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (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 1315 Processing helix chain 'D' and resid 1319 through 1325 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: 4.381A 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 75 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 113 through 135 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: 4.278A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 294 Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 314 through 321 Processing helix chain 'F' and resid 325 through 351 removed outlier: 4.099A pdb=" N HIS F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 394 removed outlier: 5.087A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 Processing helix chain 'F' and resid 427 through 446 removed outlier: 3.952A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 472 Processing helix chain 'F' and resid 480 through 486 Processing helix chain 'F' and resid 492 through 500 removed outlier: 3.874A pdb=" N LYS F 496 " --> pdb=" O ASP F 492 " (cutoff:3.500A) 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 Processing helix chain 'M' and resid 14 through 17 No H-bonds generated for 'chain 'M' and resid 14 through 17' Processing helix chain 'M' and resid 34 through 65 Processing helix chain 'M' and resid 72 through 78 removed outlier: 3.541A pdb=" N ALA M 76 " --> pdb=" O PRO M 72 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA M 77 " --> pdb=" O VAL M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 108 removed outlier: 3.572A pdb=" N LYS M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS M 98 " --> pdb=" O LYS M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 128 Processing helix chain 'M' and resid 136 through 150 Processing sheet with id= A, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.512A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105 removed outlier: 6.042A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) 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: 3.821A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 15 through 17 removed outlier: 3.571A pdb=" N LYS B 25 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.737A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.044A 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 13 through 15 Processing sheet with id= K, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= L, first strand: chain 'C' and resid 115 through 118 removed outlier: 3.895A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 143 through 145 Processing sheet with id= N, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= O, first strand: chain 'C' and resid 154 through 158 Processing sheet with id= P, first strand: chain 'C' and resid 332 through 336 removed outlier: 3.576A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 603 through 607 Processing sheet with id= R, first strand: chain 'C' and resid 633 through 637 Processing sheet with id= S, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.285A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 1096 through 1098 Processing sheet with id= U, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= V, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.590A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.278A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.601A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= Z, first strand: chain 'D' and resid 143 through 145 Processing sheet with id= AA, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= AB, first strand: chain 'D' and resid 547 through 557 Processing sheet with id= AC, first strand: chain 'D' and resid 820 through 823 Processing sheet with id= AD, first strand: chain 'D' and resid 957 through 961 Processing sheet with id= AE, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AF, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.597A pdb=" N VAL D1081 " --> pdb=" O PHE D1034 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 1162 through 1166 removed outlier: 3.996A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 4.341A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 16.26 Time building geometry restraints manager: 16.49 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: 5462 1.30 - 1.44: 8375 1.44 - 1.57: 18914 1.57 - 1.70: 236 1.70 - 1.83: 241 Bond restraints: 33228 Sorted by residual: bond pdb=" C17 1N7 D2005 " pdb=" O3 1N7 D2005 " ideal model delta sigma weight residual 0.000 1.362 -1.362 2.00e-02 2.50e+03 4.64e+03 bond pdb=" C17 1N7 C1402 " pdb=" O3 1N7 C1402 " ideal model delta sigma weight residual 0.000 1.360 -1.360 2.00e-02 2.50e+03 4.62e+03 bond pdb=" C17 1N7 C1401 " pdb=" O3 1N7 C1401 " ideal model delta sigma weight residual 0.000 1.358 -1.358 2.00e-02 2.50e+03 4.61e+03 bond pdb=" C17 1N7 D2006 " pdb=" O3 1N7 D2006 " ideal model delta sigma weight residual 0.000 1.358 -1.358 2.00e-02 2.50e+03 4.61e+03 bond pdb=" C18 1N7 C1401 " pdb=" C6 1N7 C1401 " ideal model delta sigma weight residual 0.987 1.628 -0.641 2.00e-02 2.50e+03 1.03e+03 ... (remaining 33223 not shown) Histogram of bond angle deviations from ideal: 96.48 - 103.99: 758 103.99 - 111.49: 15700 111.49 - 118.99: 12054 118.99 - 126.49: 16272 126.49 - 134.00: 559 Bond angle restraints: 45343 Sorted by residual: angle pdb=" C1' G4P M 202 " pdb=" N9 G4P M 202 " pdb=" C4 G4P M 202 " ideal model delta sigma weight residual 112.15 130.15 -18.00 3.00e+00 1.11e-01 3.60e+01 angle pdb=" C LYS D 321 " pdb=" N ARG D 322 " pdb=" CA ARG D 322 " ideal model delta sigma weight residual 120.49 128.76 -8.27 1.42e+00 4.96e-01 3.39e+01 angle pdb=" C1' G4P D2004 " pdb=" N9 G4P D2004 " pdb=" C4 G4P D2004 " ideal model delta sigma weight residual 112.15 127.05 -14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" N PRO D 926 " pdb=" CA PRO D 926 " pdb=" C PRO D 926 " ideal model delta sigma weight residual 112.47 104.20 8.27 2.06e+00 2.36e-01 1.61e+01 angle pdb=" N GLU B 229 " pdb=" CA GLU B 229 " pdb=" C GLU B 229 " ideal model delta sigma weight residual 110.80 118.90 -8.10 2.13e+00 2.20e-01 1.45e+01 ... (remaining 45338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.98: 18832 29.98 - 59.96: 1105 59.96 - 89.94: 66 89.94 - 119.92: 1 119.92 - 149.90: 2 Dihedral angle restraints: 20006 sinusoidal: 8918 harmonic: 11088 Sorted by residual: dihedral pdb=" CA ASP F 513 " pdb=" C ASP F 513 " pdb=" N ASP F 514 " pdb=" CA ASP F 514 " ideal model delta harmonic sigma weight residual 180.00 123.07 56.93 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA ILE C 198 " pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta harmonic sigma weight residual -180.00 -130.61 -49.39 0 5.00e+00 4.00e-02 9.76e+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 -136.12 -43.88 0 5.00e+00 4.00e-02 7.70e+01 ... (remaining 20003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.311: 5143 0.311 - 0.621: 9 0.621 - 0.932: 0 0.932 - 1.242: 4 1.242 - 1.553: 4 Chirality restraints: 5160 Sorted by residual: chirality pdb=" C18 1N7 D2006 " pdb=" C17 1N7 D2006 " pdb=" C19 1N7 D2006 " pdb=" C6 1N7 D2006 " both_signs ideal model delta sigma weight residual False 1.21 2.77 -1.55 2.00e-01 2.50e+01 6.03e+01 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 2.75 -1.53 2.00e-01 2.50e+01 5.87e+01 chirality pdb=" C18 1N7 D2005 " pdb=" C17 1N7 D2005 " pdb=" C19 1N7 D2005 " pdb=" C6 1N7 D2005 " both_signs ideal model delta sigma weight residual False 1.21 2.69 -1.48 2.00e-01 2.50e+01 5.45e+01 ... (remaining 5157 not shown) Planarity restraints: 5546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 42 " -0.069 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO C 43 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 426 " -0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO D 427 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT X 47 " -0.041 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" N1 DT X 47 " 0.055 2.00e-02 2.50e+03 pdb=" C2 DT X 47 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT X 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT X 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT X 47 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT X 47 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DT X 47 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT X 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT X 47 " 0.004 2.00e-02 2.50e+03 ... (remaining 5543 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 316 2.45 - 3.06: 25472 3.06 - 3.68: 48628 3.68 - 4.29: 71666 4.29 - 4.90: 114657 Nonbonded interactions: 260739 Sorted by model distance: nonbonded pdb=" O LEU D1344 " pdb=" N GLY D1346 " model vdw 1.841 2.520 nonbonded pdb=" NE2 HIS C1244 " pdb=" O PHE C1265 " model vdw 1.946 2.520 nonbonded pdb=" OE1 GLU D1030 " pdb=" OH TYR D1099 " model vdw 1.983 2.440 nonbonded pdb=" OE1 GLU D1327 " pdb=" N ARG D1330 " model vdw 1.994 2.520 nonbonded pdb=" NH2 ARG A 191 " pdb=" O ARG A 195 " model vdw 1.996 2.520 ... (remaining 260734 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 233) selection = (chain 'B' and resid 7 through 233) } 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 3 6.06 5 P 108 5.49 5 Mg 1 5.21 5 S 140 5.16 5 C 20044 2.51 5 N 5743 2.21 5 O 6488 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: 2.260 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: 12.520 Check model and map are aligned: 0.500 Convert atoms to be neutral: 0.290 Process input model: 102.990 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.022 1.362 33228 Z= 1.295 Angle : 0.999 18.001 45343 Z= 0.539 Chirality : 0.075 1.553 5160 Planarity : 0.006 0.107 5546 Dihedral : 17.271 149.898 12858 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 50.61 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.13 % Favored : 90.11 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.11), residues: 3832 helix: -1.33 (0.11), residues: 1528 sheet: -1.12 (0.24), residues: 407 loop : -2.83 (0.12), residues: 1897 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 382 time to evaluate : 3.878 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 outliers start: 8 outliers final: 5 residues processed: 388 average time/residue: 0.5733 time to fit residues: 331.1676 Evaluate side-chains 226 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 221 time to evaluate : 3.959 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2839 time to fit residues: 7.9986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.9980 chunk 297 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 307 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 355 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN C 60 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1336 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D 667 GLN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN F 446 GLN F 469 GLN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.156 33228 Z= 0.353 Angle : 0.873 12.522 45343 Z= 0.441 Chirality : 0.049 0.295 5160 Planarity : 0.006 0.101 5546 Dihedral : 17.084 143.471 5262 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.28 % Favored : 92.56 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.81 (0.12), residues: 3832 helix: 0.02 (0.12), residues: 1529 sheet: -0.79 (0.24), residues: 408 loop : -2.39 (0.12), residues: 1895 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 272 time to evaluate : 3.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 14 residues processed: 294 average time/residue: 0.4643 time to fit residues: 219.9010 Evaluate side-chains 234 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 4.134 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3259 time to fit residues: 14.3749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 chunk 356 optimal weight: 8.9990 chunk 385 optimal weight: 1.9990 chunk 317 optimal weight: 8.9990 chunk 353 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 286 optimal weight: 7.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 504 GLN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.228 33228 Z= 0.456 Angle : 0.871 15.700 45343 Z= 0.439 Chirality : 0.048 0.425 5160 Planarity : 0.006 0.121 5546 Dihedral : 17.045 142.336 5262 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.31 % Favored : 92.56 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.51 (0.13), residues: 3832 helix: 0.30 (0.12), residues: 1521 sheet: -0.59 (0.24), residues: 409 loop : -2.27 (0.13), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 222 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 21 residues processed: 262 average time/residue: 0.4273 time to fit residues: 184.4822 Evaluate side-chains 233 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 3.839 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2764 time to fit residues: 16.0870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 357 optimal weight: 2.9990 chunk 378 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 339 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.216 33228 Z= 0.457 Angle : 0.897 22.406 45343 Z= 0.443 Chirality : 0.050 1.167 5160 Planarity : 0.007 0.262 5546 Dihedral : 17.042 142.206 5262 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.20 % Favored : 92.64 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.47 (0.13), residues: 3832 helix: 0.34 (0.12), residues: 1521 sheet: -0.56 (0.24), residues: 409 loop : -2.24 (0.13), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 223 average time/residue: 0.4527 time to fit residues: 166.6860 Evaluate side-chains 219 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 3.973 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3118 time to fit residues: 10.4209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 282 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 323 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 95 optimal weight: 0.0010 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.161 33228 Z= 0.439 Angle : 0.898 27.671 45343 Z= 0.442 Chirality : 0.048 0.871 5160 Planarity : 0.007 0.181 5546 Dihedral : 17.039 142.163 5262 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.18 % Favored : 92.67 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.46 (0.13), residues: 3832 helix: 0.34 (0.12), residues: 1519 sheet: -0.55 (0.24), residues: 409 loop : -2.24 (0.13), residues: 1904 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 4.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 213 average time/residue: 0.4394 time to fit residues: 155.3648 Evaluate side-chains 211 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 3.895 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3414 time to fit residues: 5.9128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.9990 chunk 341 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 222 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 379 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.161 33228 Z= 0.439 Angle : 0.898 27.671 45343 Z= 0.442 Chirality : 0.048 0.871 5160 Planarity : 0.007 0.181 5546 Dihedral : 17.039 142.163 5262 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.18 % Favored : 92.67 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.46 (0.13), residues: 3832 helix: 0.34 (0.12), residues: 1519 sheet: -0.55 (0.24), residues: 409 loop : -2.24 (0.13), residues: 1904 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.4565 time to fit residues: 159.2912 Evaluate side-chains 211 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 4.596 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6270 time to fit residues: 6.8751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 377 optimal weight: 20.0000 chunk 236 optimal weight: 0.9980 chunk 230 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.161 33228 Z= 0.439 Angle : 0.895 27.672 45343 Z= 0.442 Chirality : 0.048 0.871 5160 Planarity : 0.007 0.181 5546 Dihedral : 17.039 142.163 5262 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.18 % Favored : 92.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.46 (0.13), residues: 3832 helix: 0.34 (0.12), residues: 1519 sheet: -0.55 (0.24), residues: 409 loop : -2.24 (0.13), residues: 1904 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 4.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.4479 time to fit residues: 156.5941 Evaluate side-chains 210 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 4.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 240 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 296 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.185 33228 Z= 0.371 Angle : 0.877 16.862 45343 Z= 0.436 Chirality : 0.047 0.477 5160 Planarity : 0.006 0.128 5546 Dihedral : 17.030 141.741 5262 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.41 (0.13), residues: 3832 helix: 0.37 (0.13), residues: 1530 sheet: -0.55 (0.24), residues: 408 loop : -2.20 (0.13), residues: 1894 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 226 average time/residue: 0.4614 time to fit residues: 170.5718 Evaluate side-chains 225 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 213 time to evaluate : 4.110 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3382 time to fit residues: 12.8023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 7.9990 chunk 361 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 352 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 153 optimal weight: 0.3980 chunk 276 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 318 optimal weight: 3.9990 chunk 332 optimal weight: 9.9990 chunk 350 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.185 33228 Z= 0.371 Angle : 0.877 16.862 45343 Z= 0.436 Chirality : 0.047 0.477 5160 Planarity : 0.006 0.128 5546 Dihedral : 17.030 141.741 5262 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.41 (0.13), residues: 3832 helix: 0.37 (0.13), residues: 1530 sheet: -0.55 (0.24), residues: 408 loop : -2.20 (0.13), residues: 1894 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 4.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.4649 time to fit residues: 163.7768 Evaluate side-chains 213 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 4.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 1.9990 chunk 372 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 390 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 240 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 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 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.185 33228 Z= 0.371 Angle : 0.877 16.851 45343 Z= 0.436 Chirality : 0.047 0.477 5160 Planarity : 0.006 0.128 5546 Dihedral : 17.030 141.741 5262 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.41 (0.13), residues: 3832 helix: 0.37 (0.13), residues: 1530 sheet: -0.55 (0.24), residues: 408 loop : -2.20 (0.13), residues: 1894 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.4559 time to fit residues: 160.2250 Evaluate side-chains 214 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 4.019 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3241 time to fit residues: 5.8376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.5980 chunk 331 optimal weight: 40.0000 chunk 95 optimal weight: 0.8980 chunk 286 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 311 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 319 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.112290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075186 restraints weight = 103443.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077800 restraints weight = 45755.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.078380 restraints weight = 26047.685| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.185 33228 Z= 0.371 Angle : 0.877 16.669 45343 Z= 0.435 Chirality : 0.047 0.477 5160 Planarity : 0.006 0.128 5546 Dihedral : 17.030 141.741 5262 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.24 % Twisted Proline : 0.67 % 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: -1.41 (0.13), residues: 3832 helix: 0.37 (0.13), residues: 1530 sheet: -0.55 (0.24), residues: 408 loop : -2.20 (0.13), residues: 1894 =============================================================================== Job complete usr+sys time: 5195.99 seconds wall clock time: 96 minutes 53.30 seconds (5813.30 seconds total)