Starting phenix.real_space_refine on Tue Feb 20 00:23:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mko_23901/02_2024/7mko_23901_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mko_23901/02_2024/7mko_23901.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mko_23901/02_2024/7mko_23901_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mko_23901/02_2024/7mko_23901_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mko_23901/02_2024/7mko_23901_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mko_23901/02_2024/7mko_23901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mko_23901/02_2024/7mko_23901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mko_23901/02_2024/7mko_23901_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mko_23901/02_2024/7mko_23901_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16253 2.51 5 N 4652 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 523": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26269 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 10414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 10414 Classifications: {'peptide': 1320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1264} Chain breaks: 1 Chain: "D" Number of atoms: 10419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10419 Classifications: {'peptide': 1344} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 55, 'TRANS': 1288} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 546 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "N" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "R" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 244 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, '2TM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14459 SG CYS D 70 18.688 104.023 76.170 1.00 78.71 S ATOM 14473 SG CYS D 72 18.980 106.965 73.987 1.00 79.04 S ATOM 14581 SG CYS D 85 16.360 104.678 73.284 1.00 73.63 S ATOM 14605 SG CYS D 88 19.900 103.740 72.560 1.00 74.07 S ATOM 20293 SG CYS D 814 33.429 37.780 77.850 1.00 41.29 S ATOM 20858 SG CYS D 888 35.339 41.067 77.440 1.00 38.47 S ATOM 20909 SG CYS D 895 34.295 39.745 80.540 1.00 34.69 S ATOM 20930 SG CYS D 898 36.728 38.164 79.128 1.00 35.95 S Time building chain proxies: 13.94, per 1000 atoms: 0.53 Number of scatterers: 26269 At special positions: 0 Unit cell: (125.4, 158.4, 163.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 63 15.00 Mg 1 11.99 O 5192 8.00 N 4652 7.00 C 16253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.18 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " Number of angles added : 12 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 32 sheets defined 33.8% alpha, 12.4% beta 22 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 12.60 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.851A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 161 removed outlier: 4.318A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 232 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 213 through 230 removed outlier: 4.629A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.336A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 328 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.761A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 481 Processing helix chain 'C' and resid 496 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 545 through 548 No H-bonds generated for 'chain 'C' and resid 545 through 548' Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 608 through 613 removed outlier: 3.606A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 657 through 660 removed outlier: 3.908A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 663 through 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: 3.953A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 820 through 824 Processing helix chain 'C' and resid 859 through 863 Processing helix chain 'C' and resid 943 through 980 removed outlier: 3.590A pdb=" N GLN C 955 " --> pdb=" O MET C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 991 removed outlier: 4.154A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 987 through 991' Processing helix chain 'C' and resid 994 through 997 Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1100 through 1104 Proline residue: C1104 - end of helix Processing helix chain 'C' and resid 1110 through 1133 Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1166 through 1178 removed outlier: 4.683A pdb=" N LYS C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1239 through 1242 No H-bonds generated for 'chain 'C' and resid 1239 through 1242' Processing helix chain 'C' and resid 1272 through 1280 Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1298 through 1309 Processing helix chain 'C' and resid 1321 through 1332 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 285 Processing helix chain 'D' and resid 289 through 308 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 370 through 387 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 415 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: 3.955A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 589 through 592 Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 614 through 635 Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 650 through 669 Processing helix chain 'D' and resid 675 through 702 Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 803 Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 915 through 934 Proline residue: D 926 - end of helix removed outlier: 3.501A pdb=" N THR D 931 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1243 Processing helix chain 'D' and resid 1250 through 1260 Processing helix chain 'D' and resid 1280 through 1292 Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1319 through 1325 removed outlier: 3.960A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1338 Processing helix chain 'D' and resid 1348 through 1353 Processing helix chain 'D' and resid 1360 through 1372 removed outlier: 4.261A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 18 through 31 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 61 through 69 Processing sheet with id= A, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.128A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.927A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= E, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.655A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 13 through 17 removed outlier: 3.888A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 170 through 172 removed outlier: 7.010A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 108 through 111 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 143 through 145 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 158 Processing sheet with id= M, first strand: chain 'C' and resid 332 through 336 removed outlier: 4.241A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 603 through 606 Processing sheet with id= O, first strand: chain 'C' and resid 633 through 637 Processing sheet with id= P, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.046A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1096 through 1098 removed outlier: 4.493A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 67 through 75 removed outlier: 6.684A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.140A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.467A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.690A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (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 143 through 146 removed outlier: 4.468A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= Y, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= Z, first strand: chain 'D' and resid 547 through 556 Processing sheet with id= AA, first strand: chain 'D' and resid 820 through 823 Processing sheet with id= AB, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.003A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1035 through 1038 Processing sheet with id= AD, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 3.896A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 1163 through 1165 removed outlier: 4.475A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 1277 through 1279 888 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 11.00 Time building geometry restraints manager: 10.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8805 1.34 - 1.47: 5846 1.47 - 1.60: 11876 1.60 - 1.73: 76 1.73 - 1.86: 186 Bond restraints: 26789 Sorted by residual: bond pdb=" C4' 2TM D2004 " pdb=" O4' 2TM D2004 " ideal model delta sigma weight residual 1.287 1.503 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C2 2TM D2004 " pdb=" O2 2TM D2004 " ideal model delta sigma weight residual 1.218 1.392 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C1' 2TM D2004 " pdb=" C2' 2TM D2004 " ideal model delta sigma weight residual 1.327 1.475 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C1' 2TM D2004 " pdb=" O4' 2TM D2004 " ideal model delta sigma weight residual 1.609 1.501 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C3' 2TM D2004 " pdb=" C4' 2TM D2004 " ideal model delta sigma weight residual 1.570 1.473 0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 26784 not shown) Histogram of bond angle deviations from ideal: 93.87 - 101.96: 166 101.96 - 110.04: 5314 110.04 - 118.13: 15545 118.13 - 126.21: 15007 126.21 - 134.29: 428 Bond angle restraints: 36460 Sorted by residual: angle pdb=" CA PRO D 758 " pdb=" N PRO D 758 " pdb=" CD PRO D 758 " ideal model delta sigma weight residual 112.00 100.93 11.07 1.40e+00 5.10e-01 6.25e+01 angle pdb=" CB ARG B 170 " pdb=" CG ARG B 170 " pdb=" CD ARG B 170 " ideal model delta sigma weight residual 111.30 126.72 -15.42 2.30e+00 1.89e-01 4.49e+01 angle pdb=" N GLU B 226 " pdb=" CA GLU B 226 " pdb=" CB GLU B 226 " ideal model delta sigma weight residual 110.12 119.67 -9.55 1.47e+00 4.63e-01 4.22e+01 angle pdb=" CB ARG C 542 " pdb=" CG ARG C 542 " pdb=" CD ARG C 542 " ideal model delta sigma weight residual 111.30 96.75 14.55 2.30e+00 1.89e-01 4.00e+01 angle pdb=" CA TRP D1020 " pdb=" CB TRP D1020 " pdb=" CG TRP D1020 " ideal model delta sigma weight residual 113.60 125.15 -11.55 1.90e+00 2.77e-01 3.69e+01 ... (remaining 36455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 15700 35.26 - 70.52: 591 70.52 - 105.78: 47 105.78 - 141.05: 1 141.05 - 176.31: 1 Dihedral angle restraints: 16340 sinusoidal: 7173 harmonic: 9167 Sorted by residual: dihedral pdb=" CA LYS C 236 " pdb=" C LYS C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 139.10 40.90 0 5.00e+00 4.00e-02 6.69e+01 dihedral pdb=" CA THR C 595 " pdb=" C THR C 595 " pdb=" N ASP C 596 " pdb=" CA ASP C 596 " ideal model delta harmonic sigma weight residual -180.00 -142.26 -37.74 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA ASP D1184 " pdb=" C ASP D1184 " pdb=" N PRO D1185 " pdb=" CA PRO D1185 " ideal model delta harmonic sigma weight residual -180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 ... (remaining 16337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3792 0.097 - 0.193: 344 0.193 - 0.290: 25 0.290 - 0.387: 4 0.387 - 0.483: 1 Chirality restraints: 4166 Sorted by residual: chirality pdb=" CB VAL C 913 " pdb=" CA VAL C 913 " pdb=" CG1 VAL C 913 " pdb=" CG2 VAL C 913 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA ARG B 170 " pdb=" N ARG B 170 " pdb=" C ARG B 170 " pdb=" CB ARG B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CG LEU D 478 " pdb=" CB LEU D 478 " pdb=" CD1 LEU D 478 " pdb=" CD2 LEU D 478 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4163 not shown) Planarity restraints: 4557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 757 " -0.141 5.00e-02 4.00e+02 2.05e-01 6.71e+01 pdb=" N PRO D 758 " 0.353 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.094 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 514 " 0.038 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE C 514 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE C 514 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 514 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 514 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 514 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 514 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 287 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 288 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " 0.055 5.00e-02 4.00e+02 ... (remaining 4554 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 5 2.00 - 2.72: 1925 2.72 - 3.45: 39542 3.45 - 4.17: 63554 4.17 - 4.90: 112140 Nonbonded interactions: 217166 Sorted by model distance: nonbonded pdb=" ND2 ASN D 910 " pdb=" O ASN E 15 " model vdw 1.275 2.520 nonbonded pdb=" OE1 GLU D 418 " pdb=" CG2 VAL E 48 " model vdw 1.523 3.460 nonbonded pdb=" ND2 ASN D 910 " pdb=" C ASN E 15 " model vdw 1.632 3.350 nonbonded pdb=" ND2 ASN D 910 " pdb=" OD1 ASN E 15 " model vdw 1.740 2.520 nonbonded pdb=" ND2 ASN D 910 " pdb=" CA ASN E 15 " model vdw 1.800 3.550 ... (remaining 217161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 235) selection = (chain 'B' and resid 7 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.210 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 80.570 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.007 0.216 26789 Z= 0.466 Angle : 1.046 18.727 36460 Z= 0.572 Chirality : 0.058 0.483 4166 Planarity : 0.007 0.205 4557 Dihedral : 17.248 176.306 10444 Min Nonbonded Distance : 1.275 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.93 % Favored : 91.60 % Rotamer: Outliers : 1.22 % Allowed : 1.29 % Favored : 97.49 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.13 % 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: -2.39 (0.13), residues: 3178 helix: -0.54 (0.14), residues: 1119 sheet: -1.03 (0.24), residues: 393 loop : -2.55 (0.12), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D1020 HIS 0.017 0.002 HIS C1070 PHE 0.069 0.003 PHE C 514 TYR 0.041 0.003 TYR D 555 ARG 0.023 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 396 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 CYS cc_start: 0.7460 (m) cc_final: 0.7106 (m) REVERT: B 142 MET cc_start: 0.7960 (ptp) cc_final: 0.7672 (ptp) REVERT: C 104 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5613 (mt) REVERT: C 1119 MET cc_start: 0.8525 (tpt) cc_final: 0.8310 (tpt) REVERT: D 604 MET cc_start: 0.8362 (ttm) cc_final: 0.8153 (ttp) REVERT: D 739 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7973 (mm-40) REVERT: D 1175 LEU cc_start: 0.6593 (mt) cc_final: 0.6161 (tt) outliers start: 33 outliers final: 2 residues processed: 417 average time/residue: 0.4202 time to fit residues: 268.3818 Evaluate side-chains 278 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 275 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 1301 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 0.6980 chunk 244 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 253 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 293 optimal weight: 9.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN C 214 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN C 761 GLN C 932 GLN C1023 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN C1313 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 861 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26789 Z= 0.275 Angle : 0.687 12.471 36460 Z= 0.353 Chirality : 0.044 0.334 4166 Planarity : 0.005 0.099 4557 Dihedral : 14.066 140.787 4223 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.92 % Favored : 93.96 % Rotamer: Outliers : 1.55 % Allowed : 9.66 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3178 helix: 0.78 (0.15), residues: 1113 sheet: -0.36 (0.24), residues: 383 loop : -1.94 (0.13), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D1193 HIS 0.012 0.001 HIS C1070 PHE 0.031 0.002 PHE C 514 TYR 0.021 0.002 TYR D 46 ARG 0.007 0.001 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 308 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 CYS cc_start: 0.7398 (m) cc_final: 0.7051 (m) REVERT: B 142 MET cc_start: 0.7894 (ptp) cc_final: 0.7637 (ptp) REVERT: C 121 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5927 (pp20) REVERT: C 370 MET cc_start: 0.7626 (mmm) cc_final: 0.7358 (mmm) REVERT: C 514 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7399 (m-10) REVERT: C 542 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7482 (mmt180) REVERT: D 201 LEU cc_start: 0.8437 (mt) cc_final: 0.8234 (mp) REVERT: D 214 ARG cc_start: 0.6813 (ttm110) cc_final: 0.6587 (ttm110) REVERT: D 475 GLU cc_start: 0.7477 (mp0) cc_final: 0.7199 (mp0) REVERT: D 1173 ARG cc_start: 0.5960 (tmm-80) cc_final: 0.4945 (ptp-110) REVERT: D 1175 LEU cc_start: 0.6790 (mt) cc_final: 0.6371 (tt) REVERT: D 1205 GLU cc_start: 0.5848 (tp30) cc_final: 0.5629 (tp30) outliers start: 42 outliers final: 28 residues processed: 336 average time/residue: 0.4023 time to fit residues: 211.4426 Evaluate side-chains 293 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 752 ASN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 317 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 291 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 235 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 462 ASN C 628 HIS C 834 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26789 Z= 0.274 Angle : 0.639 12.612 36460 Z= 0.327 Chirality : 0.043 0.253 4166 Planarity : 0.005 0.063 4557 Dihedral : 13.883 140.609 4221 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 2.36 % Allowed : 13.02 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3178 helix: 0.95 (0.15), residues: 1118 sheet: -0.17 (0.25), residues: 371 loop : -1.69 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1193 HIS 0.022 0.001 HIS C1313 PHE 0.034 0.002 PHE C 514 TYR 0.020 0.002 TYR D 46 ARG 0.004 0.001 ARG C1223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 301 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6805 (t80) REVERT: B 54 CYS cc_start: 0.7365 (m) cc_final: 0.7027 (m) REVERT: B 152 TYR cc_start: 0.8569 (t80) cc_final: 0.8292 (t80) REVERT: B 181 GLU cc_start: 0.7232 (tt0) cc_final: 0.6920 (tp30) REVERT: B 185 TYR cc_start: 0.8331 (p90) cc_final: 0.7994 (p90) REVERT: B 193 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: C 514 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: C 800 MET cc_start: 0.8113 (mtp) cc_final: 0.7777 (mtp) REVERT: C 834 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7057 (mp-120) REVERT: C 947 GLU cc_start: 0.3848 (OUTLIER) cc_final: 0.3379 (tt0) REVERT: D 201 LEU cc_start: 0.8587 (mt) cc_final: 0.8331 (mp) REVERT: D 475 GLU cc_start: 0.7484 (mp0) cc_final: 0.7231 (mp0) REVERT: D 905 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5691 (ptm160) REVERT: D 1040 MET cc_start: 0.3193 (tmm) cc_final: 0.1993 (tmm) REVERT: D 1173 ARG cc_start: 0.6091 (tmm-80) cc_final: 0.4685 (ptp-110) REVERT: D 1205 GLU cc_start: 0.6068 (tp30) cc_final: 0.5833 (tp30) REVERT: D 1325 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.6346 (p90) REVERT: E 30 MET cc_start: 0.4973 (OUTLIER) cc_final: 0.4737 (ttm) outliers start: 64 outliers final: 32 residues processed: 350 average time/residue: 0.4007 time to fit residues: 220.2575 Evaluate side-chains 309 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 269 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain E residue 30 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 312 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 279 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 158 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D 875 ASN D1279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 26789 Z= 0.412 Angle : 0.709 14.922 36460 Z= 0.365 Chirality : 0.046 0.546 4166 Planarity : 0.005 0.062 4557 Dihedral : 13.981 137.510 4221 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 3.02 % Allowed : 15.67 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3178 helix: 0.53 (0.15), residues: 1144 sheet: -0.06 (0.26), residues: 356 loop : -1.58 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 236 HIS 0.016 0.002 HIS C 554 PHE 0.046 0.002 PHE C 514 TYR 0.021 0.002 TYR D 772 ARG 0.005 0.001 ARG C1223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 283 time to evaluate : 5.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.6980 (t80) REVERT: B 7 GLU cc_start: 0.4911 (OUTLIER) cc_final: 0.4238 (pm20) REVERT: B 54 CYS cc_start: 0.7455 (m) cc_final: 0.7071 (m) REVERT: B 181 GLU cc_start: 0.7318 (tt0) cc_final: 0.6951 (tp30) REVERT: B 199 ASP cc_start: 0.6887 (p0) cc_final: 0.6557 (m-30) REVERT: C 514 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: C 626 GLU cc_start: 0.7201 (tt0) cc_final: 0.6999 (tt0) REVERT: C 785 ASP cc_start: 0.7531 (m-30) cc_final: 0.7146 (m-30) REVERT: C 800 MET cc_start: 0.8465 (mtp) cc_final: 0.7809 (mtp) REVERT: C 947 GLU cc_start: 0.4056 (OUTLIER) cc_final: 0.3650 (tt0) REVERT: C 1072 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8439 (p0) REVERT: D 135 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8137 (mm) REVERT: D 201 LEU cc_start: 0.8661 (mt) cc_final: 0.8421 (mp) REVERT: D 475 GLU cc_start: 0.7528 (mp0) cc_final: 0.7243 (mp0) REVERT: D 545 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.7525 (p-80) REVERT: D 749 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7633 (mtmm) REVERT: D 1095 MET cc_start: 0.0567 (ttt) cc_final: -0.0052 (ppp) REVERT: D 1325 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.6314 (p90) REVERT: E 30 MET cc_start: 0.4867 (OUTLIER) cc_final: 0.4644 (ttm) outliers start: 82 outliers final: 46 residues processed: 349 average time/residue: 0.3961 time to fit residues: 216.0151 Evaluate side-chains 314 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 258 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 30 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 266 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 280 optimal weight: 0.0570 chunk 78 optimal weight: 10.0000 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 834 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26789 Z= 0.204 Angle : 0.589 13.838 36460 Z= 0.302 Chirality : 0.041 0.383 4166 Planarity : 0.004 0.056 4557 Dihedral : 13.729 141.023 4221 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.88 % Favored : 93.99 % Rotamer: Outliers : 2.95 % Allowed : 16.52 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3178 helix: 0.91 (0.15), residues: 1135 sheet: 0.06 (0.27), residues: 362 loop : -1.41 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 33 HIS 0.008 0.001 HIS C1237 PHE 0.032 0.001 PHE C 514 TYR 0.015 0.001 TYR D 46 ARG 0.004 0.000 ARG D 538 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 293 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.4928 (OUTLIER) cc_final: 0.4190 (pm20) REVERT: B 54 CYS cc_start: 0.7280 (m) cc_final: 0.7041 (m) REVERT: B 148 ARG cc_start: 0.6157 (tmm160) cc_final: 0.5662 (tmm160) REVERT: B 152 TYR cc_start: 0.8473 (t80) cc_final: 0.8171 (t80) REVERT: B 181 GLU cc_start: 0.7196 (tt0) cc_final: 0.6866 (tp30) REVERT: B 185 TYR cc_start: 0.8364 (p90) cc_final: 0.7960 (p90) REVERT: C 514 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7723 (m-10) REVERT: C 798 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: C 947 GLU cc_start: 0.4029 (OUTLIER) cc_final: 0.3623 (tt0) REVERT: C 1296 ASP cc_start: 0.8665 (t0) cc_final: 0.8398 (t0) REVERT: C 1315 MET cc_start: 0.8114 (ttp) cc_final: 0.7859 (ttp) REVERT: D 135 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8048 (mm) REVERT: D 475 GLU cc_start: 0.7501 (mp0) cc_final: 0.7205 (mp0) REVERT: D 545 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7180 (p-80) REVERT: D 739 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7872 (mm-40) REVERT: D 749 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7212 (mtmm) REVERT: D 1095 MET cc_start: 0.0108 (ttt) cc_final: -0.0177 (ppp) REVERT: D 1325 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.6115 (p90) REVERT: E 30 MET cc_start: 0.4897 (OUTLIER) cc_final: 0.4642 (ttm) outliers start: 80 outliers final: 48 residues processed: 355 average time/residue: 0.3948 time to fit residues: 223.1946 Evaluate side-chains 319 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 262 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 798 GLN Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain E residue 30 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 2.9990 chunk 281 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 259 optimal weight: 0.0980 chunk 144 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 164 optimal weight: 0.0070 overall best weight: 3.0204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 437 ASN C 659 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS D 861 ASN ** D 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 26789 Z= 0.434 Angle : 0.709 14.734 36460 Z= 0.364 Chirality : 0.045 0.314 4166 Planarity : 0.005 0.064 4557 Dihedral : 13.957 137.304 4221 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.95 % Favored : 92.86 % Rotamer: Outliers : 3.24 % Allowed : 18.29 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3178 helix: 0.50 (0.15), residues: 1147 sheet: -0.15 (0.27), residues: 367 loop : -1.41 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D1193 HIS 0.012 0.001 HIS C1070 PHE 0.048 0.002 PHE C 514 TYR 0.020 0.002 TYR D 772 ARG 0.005 0.001 ARG C1177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 270 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7730 (mm110) cc_final: 0.7362 (mp10) REVERT: B 7 GLU cc_start: 0.4908 (OUTLIER) cc_final: 0.4305 (pm20) REVERT: B 148 ARG cc_start: 0.6260 (tmm160) cc_final: 0.5746 (tmm160) REVERT: B 181 GLU cc_start: 0.7285 (tt0) cc_final: 0.7068 (tp30) REVERT: B 193 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6950 (mm-30) REVERT: C 81 ASP cc_start: 0.7451 (t70) cc_final: 0.7076 (t70) REVERT: C 588 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7121 (mt-10) REVERT: C 614 TYR cc_start: 0.8661 (m-80) cc_final: 0.8454 (m-80) REVERT: C 800 MET cc_start: 0.8406 (mtp) cc_final: 0.7810 (mtp) REVERT: C 947 GLU cc_start: 0.4363 (OUTLIER) cc_final: 0.3758 (tt0) REVERT: D 135 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8247 (mm) REVERT: D 214 ARG cc_start: 0.7265 (ttm110) cc_final: 0.7048 (ttm110) REVERT: D 475 GLU cc_start: 0.7435 (mp0) cc_final: 0.7095 (mp0) REVERT: D 545 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7519 (p-80) REVERT: D 749 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7319 (mtmm) REVERT: D 1095 MET cc_start: 0.0699 (ttt) cc_final: 0.0205 (ppp) REVERT: D 1325 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.6460 (p90) REVERT: E 30 MET cc_start: 0.4926 (OUTLIER) cc_final: 0.4668 (ttm) outliers start: 88 outliers final: 54 residues processed: 336 average time/residue: 0.4020 time to fit residues: 212.0859 Evaluate side-chains 316 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 254 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 30 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 311 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 437 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 158 GLN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26789 Z= 0.267 Angle : 0.614 14.242 36460 Z= 0.314 Chirality : 0.042 0.279 4166 Planarity : 0.004 0.058 4557 Dihedral : 13.786 140.008 4220 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.14 % Favored : 93.71 % Rotamer: Outliers : 3.17 % Allowed : 18.47 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3178 helix: 0.69 (0.15), residues: 1146 sheet: -0.11 (0.26), residues: 372 loop : -1.34 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 33 HIS 0.008 0.001 HIS C1070 PHE 0.038 0.002 PHE C 514 TYR 0.015 0.001 TYR D 46 ARG 0.006 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 268 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: B 7 GLU cc_start: 0.5023 (OUTLIER) cc_final: 0.4271 (pm20) REVERT: B 122 GLU cc_start: 0.7238 (pt0) cc_final: 0.7025 (pt0) REVERT: B 148 ARG cc_start: 0.6246 (tmm160) cc_final: 0.5705 (tmm160) REVERT: B 193 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6972 (mm-30) REVERT: C 81 ASP cc_start: 0.7255 (t70) cc_final: 0.6915 (t70) REVERT: C 290 GLU cc_start: 0.7009 (pm20) cc_final: 0.6576 (pm20) REVERT: C 588 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7010 (mt-10) REVERT: C 947 GLU cc_start: 0.4564 (OUTLIER) cc_final: 0.3726 (tt0) REVERT: D 135 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8231 (mm) REVERT: D 214 ARG cc_start: 0.7253 (ttm110) cc_final: 0.7026 (ttm110) REVERT: D 475 GLU cc_start: 0.7424 (mp0) cc_final: 0.7075 (mp0) REVERT: D 545 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7378 (p-80) REVERT: D 749 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7246 (mtmm) REVERT: D 802 ASP cc_start: 0.6768 (t70) cc_final: 0.6323 (t70) REVERT: D 812 ASP cc_start: 0.7505 (t70) cc_final: 0.7235 (t0) REVERT: D 1095 MET cc_start: 0.0626 (ttt) cc_final: 0.0249 (ppp) REVERT: D 1149 ARG cc_start: 0.6828 (tpp-160) cc_final: 0.6517 (mpt-90) REVERT: D 1325 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.6165 (p90) REVERT: E 30 MET cc_start: 0.4906 (OUTLIER) cc_final: 0.4667 (ttm) outliers start: 86 outliers final: 62 residues processed: 334 average time/residue: 0.3904 time to fit residues: 205.9166 Evaluate side-chains 322 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 251 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1310 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 30 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1236 ASN D 158 GLN ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 26789 Z= 0.285 Angle : 0.622 14.799 36460 Z= 0.319 Chirality : 0.042 0.275 4166 Planarity : 0.004 0.056 4557 Dihedral : 13.734 139.884 4220 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.42 % Favored : 93.42 % Rotamer: Outliers : 3.17 % Allowed : 19.03 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3178 helix: 0.70 (0.15), residues: 1139 sheet: -0.21 (0.27), residues: 357 loop : -1.31 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1193 HIS 0.015 0.001 HIS C1237 PHE 0.038 0.002 PHE C 514 TYR 0.016 0.002 TYR D 46 ARG 0.006 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 260 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: B 7 GLU cc_start: 0.5215 (OUTLIER) cc_final: 0.4526 (pm20) REVERT: B 148 ARG cc_start: 0.6061 (tmm160) cc_final: 0.5731 (tmm160) REVERT: B 193 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: C 81 ASP cc_start: 0.7271 (t70) cc_final: 0.7025 (t70) REVERT: C 290 GLU cc_start: 0.6941 (pm20) cc_final: 0.6558 (pm20) REVERT: C 514 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7821 (m-10) REVERT: C 588 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7259 (mt-10) REVERT: C 947 GLU cc_start: 0.4514 (OUTLIER) cc_final: 0.3521 (tt0) REVERT: D 135 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8266 (mm) REVERT: D 214 ARG cc_start: 0.7284 (ttm110) cc_final: 0.7083 (ttm110) REVERT: D 475 GLU cc_start: 0.7401 (mp0) cc_final: 0.7043 (mp0) REVERT: D 545 HIS cc_start: 0.8338 (OUTLIER) cc_final: 0.7437 (p-80) REVERT: D 749 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7273 (mtmm) REVERT: D 802 ASP cc_start: 0.6769 (t70) cc_final: 0.6298 (t70) REVERT: D 812 ASP cc_start: 0.7508 (t70) cc_final: 0.7230 (t0) REVERT: D 1095 MET cc_start: 0.0952 (ttt) cc_final: 0.0579 (ppp) REVERT: D 1325 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.6095 (p90) outliers start: 86 outliers final: 67 residues processed: 325 average time/residue: 0.3944 time to fit residues: 201.7814 Evaluate side-chains 325 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 249 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 chunk 272 optimal weight: 20.0000 chunk 290 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 274 optimal weight: 9.9990 chunk 289 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 235 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 158 GLN D 196 GLN ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26789 Z= 0.190 Angle : 0.580 14.825 36460 Z= 0.296 Chirality : 0.041 0.267 4166 Planarity : 0.004 0.053 4557 Dihedral : 13.667 141.977 4220 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 2.73 % Allowed : 19.84 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3178 helix: 0.87 (0.15), residues: 1147 sheet: -0.24 (0.27), residues: 362 loop : -1.24 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.008 0.001 HIS C1237 PHE 0.029 0.001 PHE C 514 TYR 0.015 0.001 TYR D 46 ARG 0.013 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 278 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6722 (tp30) REVERT: B 7 GLU cc_start: 0.5201 (OUTLIER) cc_final: 0.4495 (pm20) REVERT: B 142 MET cc_start: 0.7773 (ptp) cc_final: 0.7510 (ptp) REVERT: B 148 ARG cc_start: 0.6060 (tmm160) cc_final: 0.5693 (tmm160) REVERT: B 152 TYR cc_start: 0.8403 (t80) cc_final: 0.8102 (t80) REVERT: B 193 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: C 81 ASP cc_start: 0.7160 (t70) cc_final: 0.6802 (t70) REVERT: C 290 GLU cc_start: 0.6878 (pm20) cc_final: 0.6506 (pm20) REVERT: C 514 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7788 (m-10) REVERT: C 588 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7034 (mt-10) REVERT: C 947 GLU cc_start: 0.4371 (OUTLIER) cc_final: 0.3546 (tt0) REVERT: D 135 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8224 (mm) REVERT: D 214 ARG cc_start: 0.7195 (ttm110) cc_final: 0.6815 (ptp-110) REVERT: D 475 GLU cc_start: 0.7451 (mp0) cc_final: 0.7036 (mp0) REVERT: D 545 HIS cc_start: 0.8329 (OUTLIER) cc_final: 0.7496 (p-80) REVERT: D 749 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7278 (mtmm) REVERT: D 802 ASP cc_start: 0.6818 (t70) cc_final: 0.6366 (t70) REVERT: D 812 ASP cc_start: 0.7419 (t70) cc_final: 0.7166 (t0) REVERT: D 1325 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.6104 (p90) outliers start: 74 outliers final: 53 residues processed: 335 average time/residue: 0.3942 time to fit residues: 208.7239 Evaluate side-chains 319 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 257 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1331 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 3.9990 chunk 306 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 196 GLN ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26789 Z= 0.195 Angle : 0.583 14.764 36460 Z= 0.298 Chirality : 0.041 0.268 4166 Planarity : 0.004 0.053 4557 Dihedral : 13.616 141.919 4220 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.74 % Rotamer: Outliers : 2.69 % Allowed : 20.10 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3178 helix: 0.92 (0.15), residues: 1146 sheet: -0.25 (0.27), residues: 362 loop : -1.22 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.004 0.001 HIS C1070 PHE 0.028 0.001 PHE C 514 TYR 0.015 0.001 TYR D 46 ARG 0.007 0.000 ARG D 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 272 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: B 7 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.4485 (pm20) REVERT: B 122 GLU cc_start: 0.7235 (pt0) cc_final: 0.7029 (pt0) REVERT: B 142 MET cc_start: 0.7756 (ptp) cc_final: 0.7514 (ptp) REVERT: B 148 ARG cc_start: 0.6049 (tmm160) cc_final: 0.5685 (tmm160) REVERT: B 152 TYR cc_start: 0.8424 (t80) cc_final: 0.8119 (t80) REVERT: B 193 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6919 (mm-30) REVERT: C 81 ASP cc_start: 0.7155 (t70) cc_final: 0.6786 (t70) REVERT: C 290 GLU cc_start: 0.6825 (pm20) cc_final: 0.6490 (pm20) REVERT: C 478 ARG cc_start: 0.8114 (ttp80) cc_final: 0.6944 (ttp80) REVERT: C 514 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: C 549 ASP cc_start: 0.8340 (t70) cc_final: 0.8136 (t0) REVERT: C 588 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7031 (mt-10) REVERT: C 947 GLU cc_start: 0.4367 (OUTLIER) cc_final: 0.3600 (tt0) REVERT: D 135 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8257 (mm) REVERT: D 214 ARG cc_start: 0.7119 (ttm110) cc_final: 0.6760 (ptp-110) REVERT: D 475 GLU cc_start: 0.7497 (mp0) cc_final: 0.7151 (mp0) REVERT: D 545 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.7538 (p-80) REVERT: D 749 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7283 (mtmm) REVERT: D 802 ASP cc_start: 0.6717 (t70) cc_final: 0.6203 (t70) REVERT: D 812 ASP cc_start: 0.7415 (t70) cc_final: 0.7160 (t0) REVERT: D 905 ARG cc_start: 0.6265 (OUTLIER) cc_final: 0.5803 (ptm160) REVERT: D 1095 MET cc_start: 0.1547 (ppp) cc_final: 0.0956 (ppp) REVERT: D 1175 LEU cc_start: 0.6631 (mt) cc_final: 0.6266 (mt) REVERT: D 1325 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.5913 (p90) outliers start: 73 outliers final: 58 residues processed: 327 average time/residue: 0.3847 time to fit residues: 199.7438 Evaluate side-chains 330 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 262 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 749 LYS Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 861 ASN Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 256 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 309 ASN ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138551 restraints weight = 34383.864| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.06 r_work: 0.3428 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 26789 Z= 0.279 Angle : 0.771 59.200 36460 Z= 0.445 Chirality : 0.052 1.848 4166 Planarity : 0.006 0.174 4557 Dihedral : 13.612 141.905 4220 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.07 % Favored : 93.74 % Rotamer: Outliers : 2.65 % Allowed : 20.43 % Favored : 76.92 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3178 helix: 0.92 (0.15), residues: 1146 sheet: -0.25 (0.27), residues: 362 loop : -1.22 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 33 HIS 0.004 0.001 HIS C1070 PHE 0.029 0.001 PHE C 514 TYR 0.015 0.001 TYR D 46 ARG 0.005 0.000 ARG D 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5799.82 seconds wall clock time: 110 minutes 44.36 seconds (6644.36 seconds total)