Starting phenix.real_space_refine on Mon Mar 11 13:26:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/03_2024/6pmi_20394_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/03_2024/6pmi_20394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/03_2024/6pmi_20394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/03_2024/6pmi_20394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/03_2024/6pmi_20394_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmi_20394/03_2024/6pmi_20394_trim_updated.pdb" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.018 sd= 0.345 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 113 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 18042 2.51 5 N 5218 2.21 5 O 5889 1.98 5 H 28610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 57985 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 21152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 21152 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1283} Chain: "D" Number of atoms: 21011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21011 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1261 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3871 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "1" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1712 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "2" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1724 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "3" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ATP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'3*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="ATP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29207 SG CYS D 70 82.000 115.253 86.755 1.00 20.00 S ATOM 29237 SG CYS D 72 82.138 118.199 84.955 1.00 20.00 S ATOM 29467 SG CYS D 85 83.046 118.637 88.108 1.00 20.00 S ATOM 29514 SG CYS D 88 79.760 118.492 88.871 1.00 20.00 S ATOM 41047 SG CYS D 814 101.947 70.561 133.594 1.00 20.00 S ATOM 42184 SG CYS D 888 99.141 70.430 131.641 1.00 20.00 S ATOM 42275 SG CYS D 895 103.449 69.075 130.891 1.00 20.00 S Time building chain proxies: 19.30, per 1000 atoms: 0.33 Number of scatterers: 57985 At special positions: 0 Unit cell: (171.9, 149.4, 180.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 113 15.00 Mg 1 11.99 O 5889 8.00 N 5218 7.00 C 18042 6.00 H 28610 1.00 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: 36.83 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 31 sheets defined 34.3% alpha, 8.9% beta 31 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 24.62 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.007A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 213 through 232 removed outlier: 3.703A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 213 through 230 removed outlier: 4.849A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 390 removed outlier: 3.790A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 479 removed outlier: 4.321A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 492 removed outlier: 3.507A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 492' Processing helix chain 'C' and resid 496 through 505 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 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 663 through 666 No H-bonds generated for 'chain 'C' and resid 663 through 666' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 688 removed outlier: 3.623A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 821 through 825 Processing helix chain 'C' and resid 859 through 864 removed outlier: 4.600A 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 980 removed outlier: 3.688A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1008 through 1037 Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1110 through 1134 removed outlier: 4.893A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY C1123 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1166 through 1178 removed outlier: 5.436A pdb=" N LYS C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1202 Processing helix chain 'C' and resid 1262 through 1264 No H-bonds generated for 'chain 'C' and resid 1262 through 1264' Processing helix chain 'C' and resid 1272 through 1281 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1309 Processing helix chain 'C' and resid 1321 through 1333 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 125 through 128 No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 133 through 139 Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.989A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.517A pdb=" N ARG D 271 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 307 removed outlier: 3.548A pdb=" N GLU D 301 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP D 304 " --> pdb=" O GLU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 378 through 388 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: 3.830A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D 456 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 530 through 539 removed outlier: 3.668A pdb=" N TYR D 537 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG D 538 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.766A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 615 through 634 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 651 through 670 Processing helix chain 'D' and resid 676 through 701 Processing helix chain 'D' and resid 721 through 728 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 788 removed outlier: 4.403A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 806 removed outlier: 5.651A pdb=" N ASP D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 873 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 916 through 929 Proline residue: D 926 - end of helix removed outlier: 4.623A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1145 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.999A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 3.746A pdb=" N VAL D1255 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE D1256 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1287 Processing helix chain 'D' and resid 1309 through 1314 removed outlier: 4.073A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1322 through 1324 No H-bonds generated for 'chain 'D' and resid 1322 through 1324' Processing helix chain 'D' and resid 1328 through 1338 removed outlier: 4.224A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 removed outlier: 3.768A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1363 through 1374 Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 17 through 31 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 61 through 79 Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.002A pdb=" N LYS F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 removed outlier: 4.182A pdb=" N ARG F 30 " --> pdb=" O HIS F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 42 through 58 Processing helix chain 'F' and resid 67 through 86 removed outlier: 4.251A pdb=" N GLN F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG F 74 " --> pdb=" O TYR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 111 Processing helix chain 'F' and resid 117 through 123 removed outlier: 3.503A pdb=" N ARG F 123 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 138 removed outlier: 3.920A pdb=" N LEU F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 188 removed outlier: 3.546A pdb=" N LEU F 173 " --> pdb=" O PRO F 169 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 removed outlier: 3.578A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 214 removed outlier: 3.549A pdb=" N VAL F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 232 Processing sheet with id= A, first strand: chain 'A' and resid 24 through 28 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: 5.662A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 110 Processing sheet with id= E, first strand: chain 'B' and resid 23 through 26 Processing sheet with id= F, first strand: chain 'B' and resid 97 through 104 removed outlier: 5.933A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 187 through 189 Processing sheet with id= H, first strand: chain 'C' and resid 12 through 14 No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= J, first strand: chain 'C' and resid 116 through 123 removed outlier: 3.608A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'C' and resid 154 through 161 Processing sheet with id= M, first strand: chain 'C' and resid 332 through 336 removed outlier: 3.899A pdb=" N LYS C 236 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 579 through 581 Processing sheet with id= O, first strand: chain 'C' and resid 634 through 638 Processing sheet with id= P, first strand: chain 'C' and resid 750 through 752 removed outlier: 5.941A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 798 through 803 Processing sheet with id= R, first strand: chain 'C' and resid 876 through 878 Processing sheet with id= S, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= T, first strand: chain 'C' and resid 931 through 935 removed outlier: 6.777A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 816 through 818 removed outlier: 8.337A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= W, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= X, first strand: chain 'D' and resid 351 through 353 Processing sheet with id= Y, first strand: chain 'D' and resid 365 through 369 removed outlier: 6.307A pdb=" N GLU D 438 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU D 368 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 440 " --> pdb=" O LEU D 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 548 through 556 Processing sheet with id= AA, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= AB, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AC, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 4.028A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.715A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 981 through 985 873 hydrogen bonds defined for protein. 2385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 20.71 Time building geometry restraints manager: 38.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 28588 1.02 - 1.22: 87 1.22 - 1.42: 12270 1.42 - 1.62: 17518 1.62 - 1.82: 192 Bond restraints: 58655 Sorted by residual: bond pdb=" C4 ATP 3 1 " pdb=" C5 ATP 3 1 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.58e+01 bond pdb=" C5 ATP 3 1 " pdb=" C6 ATP 3 1 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.46e+01 bond pdb=" C5 ATP 3 1 " pdb=" N7 ATP 3 1 " ideal model delta sigma weight residual 1.387 1.336 0.051 1.00e-02 1.00e+04 2.63e+01 bond pdb=" C ARG D1148 " pdb=" N ARG D1149 " ideal model delta sigma weight residual 1.331 1.231 0.100 2.07e-02 2.33e+03 2.34e+01 bond pdb=" C8 ATP 3 1 " pdb=" N7 ATP 3 1 " ideal model delta sigma weight residual 1.310 1.353 -0.043 1.00e-02 1.00e+04 1.85e+01 ... (remaining 58650 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.83: 710 103.83 - 111.88: 66496 111.88 - 119.93: 19738 119.93 - 127.97: 19046 127.97 - 136.02: 379 Bond angle restraints: 106369 Sorted by residual: angle pdb=" PB ATP 3 1 " pdb=" O3B ATP 3 1 " pdb=" PG ATP 3 1 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.41e+02 angle pdb=" PA ATP 3 1 " pdb=" O3A ATP 3 1 " pdb=" PB ATP 3 1 " ideal model delta sigma weight residual 136.83 117.81 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" C5 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N3 ATP 3 1 " ideal model delta sigma weight residual 126.80 117.42 9.38 1.00e+00 1.00e+00 8.81e+01 angle pdb=" N3 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N9 ATP 3 1 " ideal model delta sigma weight residual 127.04 136.02 -8.98 1.15e+00 7.59e-01 6.12e+01 angle pdb=" N VAL F 33 " pdb=" CA VAL F 33 " pdb=" C VAL F 33 " ideal model delta sigma weight residual 109.34 121.94 -12.60 2.08e+00 2.31e-01 3.67e+01 ... (remaining 106364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 25629 35.69 - 71.39: 1181 71.39 - 107.08: 17 107.08 - 142.77: 1 142.77 - 178.46: 9 Dihedral angle restraints: 26837 sinusoidal: 15841 harmonic: 10996 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual -180.00 -126.71 -53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA GLU F 151 " pdb=" C GLU F 151 " pdb=" N GLU F 152 " pdb=" CA GLU F 152 " ideal model delta harmonic sigma weight residual -180.00 -130.73 -49.27 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CA GLU B 76 " pdb=" C GLU B 76 " pdb=" N ASP B 77 " pdb=" CA ASP B 77 " ideal model delta harmonic sigma weight residual 180.00 135.80 44.20 0 5.00e+00 4.00e-02 7.81e+01 ... (remaining 26834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3570 0.072 - 0.143: 950 0.143 - 0.215: 140 0.215 - 0.287: 14 0.287 - 0.359: 1 Chirality restraints: 4675 Sorted by residual: chirality pdb=" CB VAL C 98 " pdb=" CA VAL C 98 " pdb=" CG1 VAL C 98 " pdb=" CG2 VAL C 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CG LEU F 80 " pdb=" CB LEU F 80 " pdb=" CD1 LEU F 80 " pdb=" CD2 LEU F 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE C1112 " pdb=" CA ILE C1112 " pdb=" CG1 ILE C1112 " pdb=" CG2 ILE C1112 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4672 not shown) Planarity restraints: 8383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 68 " -0.016 2.00e-02 2.50e+03 2.27e-02 1.55e+01 pdb=" CG TYR D 68 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 68 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 68 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 68 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR D 68 " 0.049 2.00e-02 2.50e+03 pdb=" CZ TYR D 68 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR D 68 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 TYR D 68 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR D 68 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR D 68 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR D 68 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 95 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C THR D 95 " 0.059 2.00e-02 2.50e+03 pdb=" O THR D 95 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS D 96 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 120 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO D 121 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.045 5.00e-02 4.00e+02 ... (remaining 8380 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 1005 2.06 - 2.69: 97489 2.69 - 3.33: 169800 3.33 - 3.96: 210826 3.96 - 4.60: 325007 Nonbonded interactions: 804127 Sorted by model distance: nonbonded pdb=" O2 DC 1 87 " pdb=" H22 DG 2 2 " model vdw 1.419 1.850 nonbonded pdb=" H ASP C 624 " pdb=" O HIS C 628 " model vdw 1.573 1.850 nonbonded pdb=" O GLU C 985 " pdb=" H LEU C 989 " model vdw 1.580 1.850 nonbonded pdb=" O ALA C 399 " pdb=" H MET C 403 " model vdw 1.593 1.850 nonbonded pdb=" OG SER C 61 " pdb=" H GLY C 64 " model vdw 1.599 1.850 ... (remaining 804122 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 6 through 233) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.640 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: 0.610 Extract box with map and model: 8.980 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 171.390 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5159 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 0.106 30045 Z= 0.782 Angle : 1.261 23.269 41067 Z= 0.735 Chirality : 0.064 0.359 4675 Planarity : 0.007 0.083 4992 Dihedral : 16.098 178.463 11826 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.74 % Favored : 88.89 % Rotamer: Outliers : 0.24 % Allowed : 4.99 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.51 % 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: -4.48 (0.11), residues: 3437 helix: -2.55 (0.11), residues: 1193 sheet: -3.28 (0.23), residues: 316 loop : -3.31 (0.12), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 807 HIS 0.018 0.004 HIS B 23 PHE 0.034 0.004 PHE C 156 TYR 0.047 0.005 TYR D 68 ARG 0.031 0.003 ARG D 799 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 536 time to evaluate : 3.324 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 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 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 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 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 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 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 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 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 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 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 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 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 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: C 912 ASP cc_start: 0.4912 (p0) cc_final: 0.4673 (p0) REVERT: C 1114 GLU cc_start: 0.5106 (pp20) cc_final: 0.4031 (pp20) REVERT: D 424 ASN cc_start: 0.6454 (t160) cc_final: 0.6214 (t0) REVERT: D 698 MET cc_start: 0.2384 (tpp) cc_final: 0.1817 (mmm) REVERT: D 917 VAL cc_start: 0.6801 (t) cc_final: 0.6506 (t) REVERT: F 151 GLU cc_start: 0.3253 (OUTLIER) cc_final: 0.1833 (tm-30) outliers start: 7 outliers final: 4 residues processed: 540 average time/residue: 1.0338 time to fit residues: 815.1130 Evaluate side-chains 372 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 367 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 834 PRO Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain F residue 151 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 275 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 319 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN C 36 GLN C 387 ASN C 752 ASN C 894 GLN C1017 GLN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN F 14 HIS ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5142 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30045 Z= 0.209 Angle : 0.726 9.363 41067 Z= 0.394 Chirality : 0.044 0.165 4675 Planarity : 0.005 0.078 4992 Dihedral : 18.659 176.273 5056 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.51 % Favored : 92.29 % Rotamer: Outliers : 1.43 % Allowed : 10.22 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.18 % 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: -3.49 (0.12), residues: 3437 helix: -1.47 (0.13), residues: 1220 sheet: -2.71 (0.25), residues: 312 loop : -2.93 (0.12), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1276 HIS 0.007 0.001 HIS D 430 PHE 0.026 0.002 PHE C 464 TYR 0.019 0.002 TYR D 723 ARG 0.007 0.001 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 418 time to evaluate : 3.372 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 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 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 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 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 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 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 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 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 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 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 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: C 912 ASP cc_start: 0.4716 (p0) cc_final: 0.4427 (p0) REVERT: F 79 MET cc_start: 0.5006 (mmm) cc_final: 0.4652 (mmm) REVERT: F 151 GLU cc_start: 0.3617 (OUTLIER) cc_final: 0.2381 (tm-30) REVERT: F 171 GLN cc_start: 0.4328 (mm-40) cc_final: 0.3931 (mm-40) outliers start: 42 outliers final: 28 residues processed: 438 average time/residue: 0.8913 time to fit residues: 588.5829 Evaluate side-chains 385 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 356 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 217 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 320 optimal weight: 8.9990 chunk 345 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 317 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS C 450 ASN C 613 ASN C 622 ASN C 725 GLN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 30045 Z= 0.396 Angle : 0.792 9.646 41067 Z= 0.441 Chirality : 0.045 0.161 4675 Planarity : 0.006 0.070 4992 Dihedral : 18.475 175.505 5053 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 27.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.94 % Favored : 88.80 % Rotamer: Outliers : 2.68 % Allowed : 12.16 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.24 % 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: -3.56 (0.12), residues: 3437 helix: -1.49 (0.13), residues: 1221 sheet: -2.63 (0.24), residues: 343 loop : -3.01 (0.12), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 868 HIS 0.009 0.002 HIS D1366 PHE 0.027 0.002 PHE C 80 TYR 0.035 0.002 TYR D 795 ARG 0.009 0.001 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 331 time to evaluate : 3.343 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 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 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 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 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 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 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 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 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 REVERT: C 912 ASP cc_start: 0.5014 (p0) cc_final: 0.4717 (p0) REVERT: C 1290 MET cc_start: 0.6367 (ptt) cc_final: 0.6163 (ptt) REVERT: D 895 CYS cc_start: 0.4058 (OUTLIER) cc_final: 0.3022 (p) REVERT: F 26 HIS cc_start: 0.3653 (OUTLIER) cc_final: 0.3434 (p-80) REVERT: F 79 MET cc_start: 0.5416 (mmm) cc_final: 0.5156 (mmp) outliers start: 79 outliers final: 64 residues processed: 381 average time/residue: 0.8485 time to fit residues: 489.1622 Evaluate side-chains 376 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 310 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 30.0000 chunk 240 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 304 optimal weight: 0.0370 chunk 91 optimal weight: 6.9990 overall best weight: 4.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN C 573 ASN C1017 GLN C1256 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30045 Z= 0.231 Angle : 0.663 8.934 41067 Z= 0.364 Chirality : 0.042 0.189 4675 Planarity : 0.005 0.062 4992 Dihedral : 18.352 176.530 5053 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.55 % Favored : 91.27 % Rotamer: Outliers : 2.58 % Allowed : 13.28 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -3.12 (0.13), residues: 3437 helix: -1.07 (0.14), residues: 1225 sheet: -2.36 (0.25), residues: 320 loop : -2.80 (0.12), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 868 HIS 0.006 0.001 HIS B 23 PHE 0.020 0.002 PHE C 464 TYR 0.020 0.001 TYR D 795 ARG 0.007 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 343 time to evaluate : 3.315 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 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 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 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 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 811 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6303 (m-40) REVERT: C 912 ASP cc_start: 0.4963 (p0) cc_final: 0.4681 (p0) REVERT: C 1141 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6075 (mt) REVERT: D 802 ASP cc_start: 0.5039 (t0) cc_final: 0.4455 (t0) REVERT: F 26 HIS cc_start: 0.3261 (OUTLIER) cc_final: 0.3040 (p-80) REVERT: F 79 MET cc_start: 0.5126 (mmm) cc_final: 0.4748 (mmm) outliers start: 76 outliers final: 55 residues processed: 390 average time/residue: 0.8872 time to fit residues: 525.7626 Evaluate side-chains 367 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 309 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1065 LYS Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1323 PHE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5492 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 30045 Z= 0.263 Angle : 0.665 8.670 41067 Z= 0.366 Chirality : 0.042 0.153 4675 Planarity : 0.005 0.108 4992 Dihedral : 18.333 176.519 5050 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.39 % Favored : 89.44 % Rotamer: Outliers : 2.82 % Allowed : 13.76 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -3.07 (0.13), residues: 3437 helix: -1.04 (0.14), residues: 1231 sheet: -2.11 (0.24), residues: 363 loop : -2.82 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 17 HIS 0.008 0.001 HIS F 225 PHE 0.022 0.002 PHE D1325 TYR 0.021 0.002 TYR D 795 ARG 0.012 0.001 ARG D1371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 326 time to evaluate : 3.366 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 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 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 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 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 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 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 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: C 811 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.6385 (m-40) REVERT: C 912 ASP cc_start: 0.5076 (p0) cc_final: 0.4822 (p0) REVERT: F 26 HIS cc_start: 0.3660 (OUTLIER) cc_final: 0.3370 (p-80) REVERT: F 79 MET cc_start: 0.5221 (mmm) cc_final: 0.4792 (mmm) REVERT: F 221 VAL cc_start: 0.6156 (t) cc_final: 0.4902 (t) outliers start: 83 outliers final: 69 residues processed: 378 average time/residue: 0.8333 time to fit residues: 482.6606 Evaluate side-chains 377 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 306 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1065 LYS Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 282 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30045 Z= 0.251 Angle : 0.656 8.391 41067 Z= 0.360 Chirality : 0.042 0.205 4675 Planarity : 0.005 0.056 4992 Dihedral : 18.344 176.713 5050 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.51 % Favored : 90.31 % Rotamer: Outliers : 3.12 % Allowed : 14.13 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -2.96 (0.13), residues: 3437 helix: -0.95 (0.14), residues: 1235 sheet: -2.11 (0.24), residues: 389 loop : -2.74 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 115 HIS 0.009 0.001 HIS F 225 PHE 0.025 0.002 PHE D1325 TYR 0.021 0.002 TYR F 20 ARG 0.008 0.001 ARG D1371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 319 time to evaluate : 3.342 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 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 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 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 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 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 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 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 revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.3425 (OUTLIER) cc_final: 0.3027 (t80) REVERT: C 811 ASN cc_start: 0.7085 (OUTLIER) cc_final: 0.6625 (m-40) REVERT: C 912 ASP cc_start: 0.5190 (p0) cc_final: 0.4935 (p0) REVERT: F 26 HIS cc_start: 0.3771 (OUTLIER) cc_final: 0.3446 (p-80) REVERT: F 79 MET cc_start: 0.5261 (mmm) cc_final: 0.4893 (mmm) outliers start: 92 outliers final: 82 residues processed: 383 average time/residue: 0.8380 time to fit residues: 494.0294 Evaluate side-chains 391 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 306 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 674 ASP Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1065 LYS Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 229 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 192 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 339 optimal weight: 20.0000 chunk 212 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30045 Z= 0.242 Angle : 0.641 7.934 41067 Z= 0.351 Chirality : 0.042 0.151 4675 Planarity : 0.005 0.056 4992 Dihedral : 18.341 176.441 5050 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.04 % Favored : 89.79 % Rotamer: Outliers : 3.02 % Allowed : 14.81 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -2.80 (0.13), residues: 3437 helix: -0.80 (0.14), residues: 1234 sheet: -2.11 (0.24), residues: 377 loop : -2.63 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 115 HIS 0.006 0.001 HIS C 628 PHE 0.025 0.002 PHE C 972 TYR 0.022 0.002 TYR F 20 ARG 0.007 0.001 ARG D1371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 309 time to evaluate : 3.358 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 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 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 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 811 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.6647 (m-40) REVERT: C 912 ASP cc_start: 0.5184 (p0) cc_final: 0.4944 (p0) REVERT: F 26 HIS cc_start: 0.3992 (OUTLIER) cc_final: 0.3682 (p-80) REVERT: F 79 MET cc_start: 0.5257 (mmm) cc_final: 0.4899 (mmm) outliers start: 89 outliers final: 80 residues processed: 370 average time/residue: 0.8208 time to fit residues: 467.6535 Evaluate side-chains 378 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 296 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 674 ASP Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1110 GLU Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30045 Z= 0.180 Angle : 0.614 8.788 41067 Z= 0.333 Chirality : 0.042 0.158 4675 Planarity : 0.004 0.072 4992 Dihedral : 18.265 175.782 5050 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.48 % Favored : 92.38 % Rotamer: Outliers : 2.82 % Allowed : 15.39 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % 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: -2.44 (0.13), residues: 3437 helix: -0.46 (0.14), residues: 1228 sheet: -2.00 (0.24), residues: 375 loop : -2.43 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 17 HIS 0.007 0.001 HIS F 225 PHE 0.015 0.001 PHE C 972 TYR 0.022 0.001 TYR F 20 ARG 0.009 0.000 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 317 time to evaluate : 3.351 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 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 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 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 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 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 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 revert: symmetry clash REVERT: B 152 TYR cc_start: 0.3607 (OUTLIER) cc_final: 0.3032 (t80) REVERT: C 42 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7253 (t0) REVERT: C 785 ASP cc_start: 0.4291 (OUTLIER) cc_final: 0.4010 (m-30) REVERT: C 811 ASN cc_start: 0.7007 (OUTLIER) cc_final: 0.6615 (m-40) REVERT: C 912 ASP cc_start: 0.5136 (p0) cc_final: 0.4890 (p0) REVERT: D 740 LEU cc_start: -0.0781 (OUTLIER) cc_final: -0.1051 (mp) REVERT: F 26 HIS cc_start: 0.3857 (OUTLIER) cc_final: 0.3595 (p-80) REVERT: F 79 MET cc_start: 0.5156 (mmm) cc_final: 0.4856 (mmm) outliers start: 83 outliers final: 70 residues processed: 367 average time/residue: 0.8099 time to fit residues: 457.8443 Evaluate side-chains 379 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 303 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 674 ASP Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1073 ASP Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 4.9990 chunk 325 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 316 optimal weight: 30.0000 chunk 324 optimal weight: 0.1980 chunk 190 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30045 Z= 0.217 Angle : 0.624 7.786 41067 Z= 0.339 Chirality : 0.041 0.152 4675 Planarity : 0.004 0.072 4992 Dihedral : 18.231 175.727 5050 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.05 % Favored : 90.81 % Rotamer: Outliers : 2.92 % Allowed : 15.76 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % 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: -2.42 (0.13), residues: 3437 helix: -0.46 (0.14), residues: 1226 sheet: -2.00 (0.25), residues: 377 loop : -2.39 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 17 HIS 0.007 0.001 HIS F 225 PHE 0.035 0.002 PHE C1323 TYR 0.020 0.001 TYR F 20 ARG 0.007 0.000 ARG D 738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 302 time to evaluate : 3.852 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 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 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.3630 (OUTLIER) cc_final: 0.3009 (t80) REVERT: C 785 ASP cc_start: 0.4301 (OUTLIER) cc_final: 0.3994 (m-30) REVERT: C 811 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6618 (m-40) REVERT: C 912 ASP cc_start: 0.5072 (p0) cc_final: 0.4832 (p0) REVERT: F 79 MET cc_start: 0.5269 (mmm) cc_final: 0.4960 (mmm) outliers start: 86 outliers final: 73 residues processed: 356 average time/residue: 0.8100 time to fit residues: 447.1130 Evaluate side-chains 369 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 293 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 674 ASP Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1073 ASP Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 350 optimal weight: 8.9990 chunk 322 optimal weight: 0.2980 chunk 279 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 952 GLN ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5541 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30045 Z= 0.204 Angle : 0.622 9.449 41067 Z= 0.336 Chirality : 0.041 0.150 4675 Planarity : 0.004 0.102 4992 Dihedral : 18.203 175.530 5046 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.18 % Favored : 91.68 % Rotamer: Outliers : 2.55 % Allowed : 16.10 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % 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: -2.34 (0.13), residues: 3437 helix: -0.39 (0.14), residues: 1228 sheet: -1.91 (0.25), residues: 377 loop : -2.36 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 17 HIS 0.007 0.001 HIS C 628 PHE 0.030 0.002 PHE C1323 TYR 0.021 0.001 TYR F 20 ARG 0.006 0.000 ARG C 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 298 time to evaluate : 3.321 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 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 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 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 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 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 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: B 152 TYR cc_start: 0.3598 (OUTLIER) cc_final: 0.2916 (t80) REVERT: C 785 ASP cc_start: 0.4278 (OUTLIER) cc_final: 0.3970 (m-30) REVERT: C 811 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6630 (m-40) REVERT: C 912 ASP cc_start: 0.5048 (p0) cc_final: 0.4812 (p0) REVERT: C 952 GLN cc_start: 0.5927 (OUTLIER) cc_final: 0.5697 (tp40) REVERT: F 79 MET cc_start: 0.5214 (mmm) cc_final: 0.4939 (mmm) outliers start: 75 outliers final: 69 residues processed: 345 average time/residue: 0.8023 time to fit residues: 430.6284 Evaluate side-chains 367 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 294 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 404 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 PHE Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 674 ASP Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 952 GLN Chi-restraints excluded: chain C residue 1009 ASN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 795 TYR Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1073 ASP Chi-restraints excluded: chain D residue 1164 SER Chi-restraints excluded: chain D residue 1239 ASP Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 279 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 287 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.083855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.062714 restraints weight = 524728.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.064984 restraints weight = 327342.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.066589 restraints weight = 236572.464| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 30045 Z= 0.337 Angle : 0.703 8.994 41067 Z= 0.385 Chirality : 0.043 0.214 4675 Planarity : 0.005 0.075 4992 Dihedral : 18.248 176.379 5046 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.70 % Favored : 88.10 % Rotamer: Outliers : 2.85 % Allowed : 16.13 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % 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: -2.80 (0.13), residues: 3437 helix: -0.88 (0.14), residues: 1224 sheet: -2.12 (0.24), residues: 379 loop : -2.55 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C1276 HIS 0.010 0.002 HIS C 628 PHE 0.029 0.002 PHE C 629 TYR 0.021 0.002 TYR F 20 ARG 0.009 0.001 ARG D 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10916.18 seconds wall clock time: 190 minutes 1.47 seconds (11401.47 seconds total)