Starting phenix.real_space_refine on Tue Feb 20 00:07:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eha_28145/02_2024/8eha_28145_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eha_28145/02_2024/8eha_28145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eha_28145/02_2024/8eha_28145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eha_28145/02_2024/8eha_28145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eha_28145/02_2024/8eha_28145_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eha_28145/02_2024/8eha_28145_updated.pdb" } resolution = 3.7 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= 0.005 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 16259 2.51 5 N 4641 2.21 5 O 5178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 214": "OE1" <-> "OE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H GLU 229": "OE1" <-> "OE2" Residue "I GLU 7": "OE1" <-> "OE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I GLU 386": "OE1" <-> "OE2" Residue "I GLU 541": "OE1" <-> "OE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I GLU 940": "OE1" <-> "OE2" Residue "I GLU 947": "OE1" <-> "OE2" Residue "I GLU 963": "OE1" <-> "OE2" Residue "I TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1024": "OE1" <-> "OE2" Residue "I GLU 1083": "OE1" <-> "OE2" Residue "I GLU 1167": "OE1" <-> "OE2" Residue "I GLU 1321": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 532": "OE1" <-> "OE2" Residue "J GLU 765": "OE1" <-> "OE2" Residue "J GLU 866": "OE1" <-> "OE2" Residue "J GLU 925": "OE1" <-> "OE2" Residue "J GLU 981": "OE1" <-> "OE2" Residue "J GLU 1187": "OE1" <-> "OE2" Residue "J GLU 1188": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J GLU 1317": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 74": "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: 26250 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10371 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 10541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10541 Classifications: {'peptide': 1358} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15501 SG CYS J 70 105.714 101.302 89.302 1.00 86.03 S ATOM 15515 SG CYS J 72 106.137 105.046 89.685 1.00 93.36 S ATOM 15623 SG CYS J 85 107.825 102.735 92.115 1.00 92.75 S ATOM 15647 SG CYS J 88 104.079 102.968 92.255 1.00 90.67 S ATOM 21335 SG CYS J 814 87.623 36.796 85.517 1.00 51.34 S ATOM 21900 SG CYS J 888 86.076 40.281 86.040 1.00 45.23 S ATOM 21951 SG CYS J 895 87.068 39.081 82.561 1.00 43.74 S ATOM 21972 SG CYS J 898 84.093 37.581 84.308 1.00 42.91 S Time building chain proxies: 13.25, per 1000 atoms: 0.50 Number of scatterers: 26250 At special positions: 0 Unit cell: (139.1, 149.5, 162.5, 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 5178 8.00 N 4641 7.00 C 16259 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: 10.45 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 12 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 36 sheets defined 31.4% alpha, 11.7% beta 30 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 13.56 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 230 removed outlier: 4.243A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 229 removed outlier: 3.730A pdb=" N GLU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 39 Processing helix chain 'I' and resid 49 through 56 removed outlier: 3.736A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 164 through 166 No H-bonds generated for 'chain 'I' and resid 164 through 166' Processing helix chain 'I' and resid 207 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.604A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.986A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 328 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.924A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 448 through 450 No H-bonds generated for 'chain 'I' and resid 448 through 450' Processing helix chain 'I' and resid 456 through 481 removed outlier: 3.779A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 526 Processing helix chain 'I' and resid 545 through 548 No H-bonds generated for 'chain 'I' and resid 545 through 548' Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 657 through 660 removed outlier: 3.923A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 657 through 660' Processing helix chain 'I' and resid 664 through 666 No H-bonds generated for 'chain 'I' and resid 664 through 666' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 687 Processing helix chain 'I' and resid 705 through 712 Processing helix chain 'I' and resid 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 943 through 979 removed outlier: 3.767A pdb=" N LEU I 960 " --> pdb=" O ALA I 956 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1036 Processing helix chain 'I' and resid 1100 through 1104 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1109 through 1133 removed outlier: 3.527A pdb=" N LEU I1113 " --> pdb=" O GLY I1110 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS I1133 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1168 through 1176 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1281 removed outlier: 3.586A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1299 through 1310 Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.729A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 195 through 207 Processing helix chain 'J' and resid 212 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 265 through 284 removed outlier: 3.631A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 328 through 330 No H-bonds generated for 'chain 'J' and resid 328 through 330' Processing helix chain 'J' and resid 370 through 376 removed outlier: 3.768A pdb=" N LEU J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 408 through 415 removed outlier: 4.357A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 3.524A pdb=" N CYS J 454 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR J 457 " --> pdb=" O CYS J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 582 removed outlier: 3.690A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE J 582 " --> pdb=" O ILE J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 611 Processing helix chain 'J' and resid 615 through 633 removed outlier: 3.522A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 651 through 669 Processing helix chain 'J' and resid 677 through 701 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 771 through 803 removed outlier: 3.790A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER J 793 " --> pdb=" O LYS J 789 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR J 797 " --> pdb=" O SER J 793 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 866 through 874 removed outlier: 4.193A pdb=" N GLU J 873 " --> pdb=" O CYS J 869 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 924 Processing helix chain 'J' and resid 927 through 931 Processing helix chain 'J' and resid 934 through 936 No H-bonds generated for 'chain 'J' and resid 934 through 936' Processing helix chain 'J' and resid 1140 through 1146 Processing helix chain 'J' and resid 1219 through 1244 removed outlier: 3.541A pdb=" N GLY J1225 " --> pdb=" O LEU J1221 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1311 through 1314 No H-bonds generated for 'chain 'J' and resid 1311 through 1314' Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1338 removed outlier: 3.636A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1363 through 1371 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 79 removed outlier: 3.616A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 187 through 189 removed outlier: 3.984A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 97 through 99 removed outlier: 3.868A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 102 through 104 removed outlier: 3.673A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 108 through 110 removed outlier: 3.566A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 151 through 153 Processing sheet with id= F, first strand: chain 'G' and resid 180 through 184 removed outlier: 6.622A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 12 through 15 removed outlier: 3.566A pdb=" N ARG H 12 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU H 29 " --> pdb=" O ARG H 12 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.527A pdb=" N GLU H 60 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 108 through 111 Processing sheet with id= J, first strand: chain 'I' and resid 66 through 69 removed outlier: 3.764A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN I 120 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS I 118 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 73 through 75 Processing sheet with id= L, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= M, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= N, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= O, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.746A pdb=" N ASN I 173 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 185 through 188 Processing sheet with id= Q, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= R, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= S, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= T, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.545A pdb=" N ASP I 749 " --> pdb=" O ILE I 734 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.466A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 930 through 935 removed outlier: 3.987A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 1065 through 1067 Processing sheet with id= X, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.650A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.695A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.700A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AB, first strand: chain 'J' and resid 548 through 556 Processing sheet with id= AC, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AD, first strand: chain 'J' and resid 956 through 961 removed outlier: 3.959A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP J 986 " --> pdb=" O THR J 991 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR J 991 " --> pdb=" O ASP J 986 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AF, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.646A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 1046 through 1050 Processing sheet with id= AH, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AI, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.454A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.812A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2154 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 11.50 Time building geometry restraints manager: 11.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8672 1.34 - 1.46: 4701 1.46 - 1.58: 13087 1.58 - 1.70: 126 1.70 - 1.82: 187 Bond restraints: 26773 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.822 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.727 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.705 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C19 1N7 I1401 " pdb=" C2 1N7 I1401 " ideal model delta sigma weight residual 1.551 1.398 0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" C4 1N7 I1401 " pdb=" C5 1N7 I1401 " ideal model delta sigma weight residual 1.534 1.394 0.140 2.00e-02 2.50e+03 4.93e+01 ... (remaining 26768 not shown) Histogram of bond angle deviations from ideal: 97.54 - 104.87: 678 104.87 - 112.21: 13635 112.21 - 119.54: 9309 119.54 - 126.88: 12451 126.88 - 134.21: 369 Bond angle restraints: 36442 Sorted by residual: angle pdb=" C ILE I1079 " pdb=" N ASN I1080 " pdb=" CA ASN I1080 " ideal model delta sigma weight residual 120.49 127.67 -7.18 1.42e+00 4.96e-01 2.56e+01 angle pdb=" N ARG J 764 " pdb=" CA ARG J 764 " pdb=" C ARG J 764 " ideal model delta sigma weight residual 113.18 107.24 5.94 1.33e+00 5.65e-01 2.00e+01 angle pdb=" C VAL J 518 " pdb=" N ASN J 519 " pdb=" CA ASN J 519 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 angle pdb=" N GLN I 46 " pdb=" CA GLN I 46 " pdb=" C GLN I 46 " ideal model delta sigma weight residual 114.75 110.27 4.48 1.26e+00 6.30e-01 1.27e+01 angle pdb=" C ARG J 709 " pdb=" N ASP J 710 " pdb=" CA ASP J 710 " ideal model delta sigma weight residual 125.02 131.26 -6.24 1.76e+00 3.23e-01 1.26e+01 ... (remaining 36437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 15853 35.26 - 70.51: 518 70.51 - 105.77: 27 105.77 - 141.03: 2 141.03 - 176.29: 2 Dihedral angle restraints: 16402 sinusoidal: 7251 harmonic: 9151 Sorted by residual: dihedral pdb=" CA GLU J 925 " pdb=" C GLU J 925 " pdb=" N PRO J 926 " pdb=" CA PRO J 926 " ideal model delta harmonic sigma weight residual 180.00 144.14 35.86 0 5.00e+00 4.00e-02 5.14e+01 dihedral pdb=" CA LEU J1138 " pdb=" C LEU J1138 " pdb=" N PRO J1139 " pdb=" CA PRO J1139 " ideal model delta harmonic sigma weight residual 180.00 146.93 33.07 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA VAL I1309 " pdb=" C VAL I1309 " pdb=" N ASP I1310 " pdb=" CA ASP I1310 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 16399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3863 0.082 - 0.163: 308 0.163 - 0.245: 3 0.245 - 0.327: 1 0.327 - 0.409: 1 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.94 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C15 1N7 I1401 " pdb=" C14 1N7 I1401 " pdb=" C16 1N7 I1401 " pdb=" C2 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C5 1N7 I1401 " pdb=" C4 1N7 I1401 " pdb=" C6 1N7 I1401 " pdb=" C9 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.85 -2.61 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4173 not shown) Planarity restraints: 4545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 925 " -0.056 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO J 926 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO J 926 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 926 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J1138 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO J1139 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO J1139 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO J1139 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO J 851 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.034 5.00e-02 4.00e+02 ... (remaining 4542 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 249 2.58 - 3.16: 21055 3.16 - 3.74: 41380 3.74 - 4.32: 55225 4.32 - 4.90: 92730 Nonbonded interactions: 210639 Sorted by model distance: nonbonded pdb=" O3' C R 18 " pdb="MG MG R 101 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG R 101 " model vdw 2.038 2.170 nonbonded pdb=" O6 DG A 3 " pdb=" N6 DA B 29 " model vdw 2.077 2.520 nonbonded pdb=" NH2 ARG I 528 " pdb=" O SER I 576 " model vdw 2.196 2.520 nonbonded pdb=" O TRP J 115 " pdb=" OG SER J 119 " model vdw 2.216 2.440 ... (remaining 210634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 231)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 5.300 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 79.310 Find NCS groups from input model: 1.190 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: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.005 0.290 26773 Z= 0.310 Angle : 0.615 10.396 36442 Z= 0.340 Chirality : 0.043 0.409 4176 Planarity : 0.004 0.085 4545 Dihedral : 15.479 176.286 10518 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.77 % Allowed : 9.69 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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: -1.50 (0.14), residues: 3174 helix: 0.23 (0.16), residues: 1071 sheet: -1.36 (0.28), residues: 369 loop : -1.75 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 580 HIS 0.005 0.001 HIS G 23 PHE 0.013 0.001 PHE I 514 TYR 0.013 0.001 TYR J 723 ARG 0.005 0.000 ARG J 709 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 421 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 LEU cc_start: 0.8737 (tp) cc_final: 0.8396 (tp) REVERT: I 195 PHE cc_start: 0.8124 (m-10) cc_final: 0.7827 (m-10) REVERT: I 423 ASP cc_start: 0.7499 (p0) cc_final: 0.6937 (p0) REVERT: I 434 ASP cc_start: 0.8097 (m-30) cc_final: 0.7781 (m-30) REVERT: I 459 MET cc_start: 0.8914 (mtp) cc_final: 0.8683 (mtp) REVERT: I 704 MET cc_start: 0.8428 (tpp) cc_final: 0.8108 (tpp) REVERT: I 930 ASP cc_start: 0.7275 (m-30) cc_final: 0.6977 (m-30) REVERT: I 940 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: I 941 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7029 (mtmm) REVERT: I 997 TRP cc_start: 0.6652 (m100) cc_final: 0.6037 (m100) REVERT: I 1240 ASP cc_start: 0.8036 (p0) cc_final: 0.7786 (p0) REVERT: I 1290 MET cc_start: 0.8700 (mmt) cc_final: 0.8471 (mmt) REVERT: J 92 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8044 (p) REVERT: J 227 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8672 (m-80) REVERT: J 308 ASP cc_start: 0.8710 (t0) cc_final: 0.8418 (t0) REVERT: J 644 MET cc_start: 0.8750 (mtt) cc_final: 0.8120 (mtt) REVERT: J 697 MET cc_start: 0.8671 (ttp) cc_final: 0.8415 (ttp) REVERT: J 698 MET cc_start: 0.7805 (tpt) cc_final: 0.7090 (tpt) REVERT: J 706 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7999 (m) REVERT: J 806 ASP cc_start: 0.7829 (p0) cc_final: 0.7514 (p0) REVERT: J 822 MET cc_start: 0.8978 (mmt) cc_final: 0.8660 (mmt) REVERT: J 831 VAL cc_start: 0.7825 (OUTLIER) cc_final: 0.7383 (m) REVERT: J 1158 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6486 (tm-30) REVERT: J 1159 ILE cc_start: 0.9140 (tp) cc_final: 0.8890 (tp) outliers start: 102 outliers final: 49 residues processed: 502 average time/residue: 0.3924 time to fit residues: 316.7521 Evaluate side-chains 390 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 335 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 940 GLU Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 30.0000 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS H 103 ASN I 554 HIS I 737 ASN I 965 GLN I1023 HIS J 424 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26773 Z= 0.333 Angle : 0.594 8.549 36442 Z= 0.307 Chirality : 0.043 0.187 4176 Planarity : 0.004 0.091 4545 Dihedral : 15.163 176.816 4391 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.62 % Allowed : 13.23 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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: -1.40 (0.15), residues: 3174 helix: 0.52 (0.16), residues: 1090 sheet: -1.59 (0.26), residues: 396 loop : -1.78 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 PHE 0.012 0.001 PHE J 437 TYR 0.014 0.001 TYR G 152 ARG 0.007 0.000 ARG I 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 350 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 28 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8869 (pt) REVERT: H 102 LEU cc_start: 0.8467 (tp) cc_final: 0.8135 (tp) REVERT: I 39 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9131 (tp) REVERT: I 68 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8033 (tp) REVERT: I 434 ASP cc_start: 0.8153 (m-30) cc_final: 0.7820 (m-30) REVERT: I 488 MET cc_start: 0.8286 (mmp) cc_final: 0.7641 (mmm) REVERT: I 930 ASP cc_start: 0.7309 (m-30) cc_final: 0.7059 (m-30) REVERT: I 1085 MET cc_start: 0.9025 (mmm) cc_final: 0.8583 (mmp) REVERT: I 1107 MET cc_start: 0.7992 (mtm) cc_final: 0.7755 (mtm) REVERT: I 1240 ASP cc_start: 0.8121 (p0) cc_final: 0.7848 (p0) REVERT: J 100 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6966 (tm-30) REVERT: J 227 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8699 (m-80) REVERT: J 308 ASP cc_start: 0.8756 (t0) cc_final: 0.8382 (t0) REVERT: J 644 MET cc_start: 0.8837 (mtt) cc_final: 0.8323 (mtt) REVERT: J 698 MET cc_start: 0.7816 (tpt) cc_final: 0.7209 (tpt) REVERT: J 706 VAL cc_start: 0.8241 (m) cc_final: 0.8021 (m) REVERT: J 806 ASP cc_start: 0.7754 (p0) cc_final: 0.7468 (p0) REVERT: J 822 MET cc_start: 0.8831 (mmt) cc_final: 0.8449 (mmt) REVERT: J 1158 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6416 (tm-30) REVERT: J 1159 ILE cc_start: 0.9195 (tp) cc_final: 0.8745 (tp) outliers start: 125 outliers final: 97 residues processed: 444 average time/residue: 0.3534 time to fit residues: 253.4644 Evaluate side-chains 425 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 324 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 135 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1195 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 289 optimal weight: 0.3980 chunk 99 optimal weight: 0.0470 chunk 234 optimal weight: 3.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 128 HIS I 737 ASN I1023 HIS K 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26773 Z= 0.152 Angle : 0.516 10.788 36442 Z= 0.266 Chirality : 0.041 0.166 4176 Planarity : 0.004 0.089 4545 Dihedral : 14.720 175.860 4375 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.14 % Allowed : 14.90 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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: -1.16 (0.15), residues: 3174 helix: 0.77 (0.16), residues: 1086 sheet: -1.45 (0.26), residues: 404 loop : -1.67 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 580 HIS 0.007 0.001 HIS I1023 PHE 0.010 0.001 PHE J 437 TYR 0.019 0.001 TYR G 152 ARG 0.005 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 365 time to evaluate : 3.017 Fit side-chains revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6331 (p0) REVERT: G 202 VAL cc_start: 0.9444 (t) cc_final: 0.9184 (p) REVERT: H 79 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8369 (mm) REVERT: I 39 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9074 (tp) REVERT: I 434 ASP cc_start: 0.8120 (m-30) cc_final: 0.7766 (m-30) REVERT: I 459 MET cc_start: 0.9079 (mtp) cc_final: 0.8539 (mtp) REVERT: I 463 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: I 488 MET cc_start: 0.8290 (mmp) cc_final: 0.7243 (tpt) REVERT: I 737 ASN cc_start: 0.8023 (m110) cc_final: 0.7745 (m-40) REVERT: I 930 ASP cc_start: 0.7312 (m-30) cc_final: 0.7045 (m-30) REVERT: I 997 TRP cc_start: 0.6909 (m100) cc_final: 0.6097 (m100) REVERT: I 1085 MET cc_start: 0.9068 (mmm) cc_final: 0.8619 (mmp) REVERT: I 1107 MET cc_start: 0.7924 (mtm) cc_final: 0.7693 (mtm) REVERT: I 1240 ASP cc_start: 0.8047 (p0) cc_final: 0.7718 (p0) REVERT: I 1265 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7299 (t80) REVERT: J 227 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8608 (m-80) REVERT: J 308 ASP cc_start: 0.8718 (t0) cc_final: 0.8460 (t0) REVERT: J 560 ASN cc_start: 0.6268 (p0) cc_final: 0.5964 (p0) REVERT: J 644 MET cc_start: 0.8734 (mtt) cc_final: 0.8174 (mtt) REVERT: J 697 MET cc_start: 0.8587 (ttp) cc_final: 0.8196 (ttp) REVERT: J 698 MET cc_start: 0.7934 (tpt) cc_final: 0.6990 (tpt) REVERT: J 702 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.6206 (pp30) REVERT: J 706 VAL cc_start: 0.8179 (m) cc_final: 0.7963 (m) REVERT: J 802 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: J 806 ASP cc_start: 0.7781 (p0) cc_final: 0.7491 (p0) REVERT: J 822 MET cc_start: 0.8872 (mmt) cc_final: 0.8460 (mmt) REVERT: J 1158 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6288 (tm-30) REVERT: J 1159 ILE cc_start: 0.9143 (tp) cc_final: 0.8658 (tp) REVERT: K 73 GLN cc_start: 0.7247 (pp30) cc_final: 0.7013 (pp30) outliers start: 112 outliers final: 77 residues processed: 450 average time/residue: 0.3654 time to fit residues: 264.6947 Evaluate side-chains 418 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 333 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 277 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1023 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26773 Z= 0.227 Angle : 0.537 8.142 36442 Z= 0.276 Chirality : 0.041 0.170 4176 Planarity : 0.004 0.086 4545 Dihedral : 14.670 177.096 4370 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.06 % Allowed : 15.86 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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 (0.15), residues: 3174 helix: 0.81 (0.16), residues: 1086 sheet: -1.37 (0.26), residues: 404 loop : -1.63 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.006 0.001 HIS I1023 PHE 0.010 0.001 PHE I 514 TYR 0.018 0.001 TYR I 70 ARG 0.005 0.000 ARG I 779 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 347 time to evaluate : 2.904 Fit side-chains revert: symmetry clash REVERT: G 68 TYR cc_start: 0.9076 (m-80) cc_final: 0.8765 (m-10) REVERT: G 111 THR cc_start: 0.9151 (p) cc_final: 0.8886 (p) REVERT: G 120 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6330 (p0) REVERT: G 202 VAL cc_start: 0.9470 (t) cc_final: 0.9215 (p) REVERT: H 28 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8932 (pt) REVERT: H 79 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8387 (mm) REVERT: H 80 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8117 (mt-10) REVERT: I 39 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9102 (tp) REVERT: I 434 ASP cc_start: 0.8145 (m-30) cc_final: 0.7809 (m-30) REVERT: I 459 MET cc_start: 0.9095 (mtp) cc_final: 0.8586 (mtp) REVERT: I 463 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: I 488 MET cc_start: 0.8375 (mmp) cc_final: 0.7365 (tpt) REVERT: I 518 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8696 (p0) REVERT: I 737 ASN cc_start: 0.8066 (m110) cc_final: 0.7793 (m-40) REVERT: I 930 ASP cc_start: 0.7290 (m-30) cc_final: 0.7047 (m-30) REVERT: I 997 TRP cc_start: 0.6950 (m100) cc_final: 0.6135 (m100) REVERT: I 1085 MET cc_start: 0.9095 (mmm) cc_final: 0.8853 (mmm) REVERT: I 1107 MET cc_start: 0.7974 (mtm) cc_final: 0.7761 (mtm) REVERT: I 1240 ASP cc_start: 0.8079 (p0) cc_final: 0.7762 (p0) REVERT: I 1265 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7518 (t80) REVERT: J 227 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: J 308 ASP cc_start: 0.8751 (t0) cc_final: 0.8380 (t0) REVERT: J 560 ASN cc_start: 0.6312 (p0) cc_final: 0.6001 (p0) REVERT: J 644 MET cc_start: 0.8822 (mtt) cc_final: 0.8373 (mtt) REVERT: J 697 MET cc_start: 0.8655 (ttp) cc_final: 0.8304 (ttp) REVERT: J 698 MET cc_start: 0.7955 (tpt) cc_final: 0.6987 (tpt) REVERT: J 702 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.6334 (pp30) REVERT: J 706 VAL cc_start: 0.8209 (m) cc_final: 0.7998 (m) REVERT: J 802 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: J 806 ASP cc_start: 0.7745 (p0) cc_final: 0.7471 (p0) REVERT: J 822 MET cc_start: 0.8816 (mmt) cc_final: 0.8408 (mmt) REVERT: J 1158 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6273 (tm-30) REVERT: J 1159 ILE cc_start: 0.9069 (tp) cc_final: 0.8446 (tp) REVERT: K 74 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6320 (mp0) outliers start: 137 outliers final: 93 residues processed: 453 average time/residue: 0.3761 time to fit residues: 275.5984 Evaluate side-chains 435 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 332 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 0.9990 chunk 278 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 ASN G 93 GLN I 673 HIS I1017 GLN I1023 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26773 Z= 0.310 Angle : 0.583 11.569 36442 Z= 0.297 Chirality : 0.042 0.177 4176 Planarity : 0.004 0.090 4545 Dihedral : 14.721 178.554 4367 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.36 % Allowed : 16.60 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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: -1.12 (0.15), residues: 3174 helix: 0.75 (0.16), residues: 1099 sheet: -1.39 (0.26), residues: 400 loop : -1.64 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.006 0.001 HIS I1023 PHE 0.010 0.001 PHE I 35 TYR 0.021 0.001 TYR G 152 ARG 0.006 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 341 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8793 (ptpp) REVERT: G 68 TYR cc_start: 0.9121 (m-80) cc_final: 0.8860 (m-10) REVERT: G 111 THR cc_start: 0.9148 (p) cc_final: 0.8884 (p) REVERT: G 120 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6312 (p0) REVERT: G 202 VAL cc_start: 0.9494 (t) cc_final: 0.9285 (p) REVERT: H 28 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8924 (pt) REVERT: H 79 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8378 (mm) REVERT: I 434 ASP cc_start: 0.8167 (m-30) cc_final: 0.7822 (m-30) REVERT: I 459 MET cc_start: 0.9109 (mtp) cc_final: 0.8571 (mtp) REVERT: I 463 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: I 488 MET cc_start: 0.8451 (mmp) cc_final: 0.7444 (tpt) REVERT: I 518 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8840 (p0) REVERT: I 930 ASP cc_start: 0.7234 (m-30) cc_final: 0.7003 (m-30) REVERT: I 1085 MET cc_start: 0.9083 (mmm) cc_final: 0.8756 (mmm) REVERT: I 1107 MET cc_start: 0.8016 (mtm) cc_final: 0.7804 (mtm) REVERT: I 1240 ASP cc_start: 0.8158 (p0) cc_final: 0.7858 (p0) REVERT: I 1265 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7702 (t80) REVERT: J 227 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: J 308 ASP cc_start: 0.8743 (t0) cc_final: 0.8362 (t0) REVERT: J 330 MET cc_start: 0.7924 (ptp) cc_final: 0.7627 (ptp) REVERT: J 644 MET cc_start: 0.8889 (mtt) cc_final: 0.8499 (mtt) REVERT: J 698 MET cc_start: 0.7835 (tpt) cc_final: 0.6951 (tpt) REVERT: J 702 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.6486 (pp30) REVERT: J 802 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: J 806 ASP cc_start: 0.7751 (p0) cc_final: 0.7506 (p0) REVERT: J 822 MET cc_start: 0.8772 (mmt) cc_final: 0.8341 (mmt) REVERT: J 832 LYS cc_start: 0.7490 (mttt) cc_final: 0.7226 (mttp) REVERT: J 898 CYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7859 (m) REVERT: J 925 GLU cc_start: 0.8522 (pp20) cc_final: 0.8211 (pp20) REVERT: J 936 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6337 (m90) REVERT: J 1158 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6424 (tm-30) outliers start: 145 outliers final: 109 residues processed: 450 average time/residue: 0.3482 time to fit residues: 253.4590 Evaluate side-chains 447 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 327 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 936 HIS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.6980 chunk 279 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 163 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 737 ASN I1023 HIS J1098 GLN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26773 Z= 0.179 Angle : 0.538 11.888 36442 Z= 0.273 Chirality : 0.041 0.182 4176 Planarity : 0.004 0.088 4545 Dihedral : 14.590 177.400 4363 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.70 % Allowed : 18.08 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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: -0.94 (0.15), residues: 3174 helix: 0.99 (0.16), residues: 1085 sheet: -1.19 (0.27), residues: 392 loop : -1.61 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 580 HIS 0.007 0.001 HIS I1023 PHE 0.009 0.001 PHE J 437 TYR 0.018 0.001 TYR G 152 ARG 0.008 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 357 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9063 (mtmm) cc_final: 0.8796 (ptpp) REVERT: G 68 TYR cc_start: 0.9054 (m-80) cc_final: 0.8771 (m-10) REVERT: G 111 THR cc_start: 0.9120 (p) cc_final: 0.8853 (p) REVERT: G 202 VAL cc_start: 0.9451 (t) cc_final: 0.9198 (p) REVERT: H 28 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8880 (pt) REVERT: H 79 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8587 (mm) REVERT: I 459 MET cc_start: 0.9039 (mtp) cc_final: 0.8531 (mtp) REVERT: I 463 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: I 488 MET cc_start: 0.8397 (mmp) cc_final: 0.7414 (tpt) REVERT: I 518 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8581 (p0) REVERT: I 737 ASN cc_start: 0.8070 (m110) cc_final: 0.7722 (m-40) REVERT: I 930 ASP cc_start: 0.7221 (m-30) cc_final: 0.7017 (m-30) REVERT: I 1085 MET cc_start: 0.9083 (mmm) cc_final: 0.8788 (mmm) REVERT: I 1240 ASP cc_start: 0.8157 (p0) cc_final: 0.7821 (p0) REVERT: I 1265 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7548 (t80) REVERT: J 227 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: J 308 ASP cc_start: 0.8733 (t0) cc_final: 0.8360 (t0) REVERT: J 330 MET cc_start: 0.7990 (ptp) cc_final: 0.7640 (ptp) REVERT: J 643 ASP cc_start: 0.8704 (m-30) cc_final: 0.8378 (m-30) REVERT: J 644 MET cc_start: 0.8771 (mtt) cc_final: 0.8330 (mtt) REVERT: J 697 MET cc_start: 0.8654 (ttp) cc_final: 0.8214 (ttp) REVERT: J 698 MET cc_start: 0.7892 (tpt) cc_final: 0.6956 (tpt) REVERT: J 702 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.6320 (pp30) REVERT: J 802 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: J 806 ASP cc_start: 0.7710 (p0) cc_final: 0.7489 (p0) REVERT: J 822 MET cc_start: 0.8869 (mmt) cc_final: 0.8435 (mmt) REVERT: J 832 LYS cc_start: 0.7655 (mttt) cc_final: 0.7372 (mttp) REVERT: J 898 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7762 (m) REVERT: J 936 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6363 (m90) REVERT: J 1158 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6321 (tm-30) outliers start: 127 outliers final: 101 residues processed: 455 average time/residue: 0.3623 time to fit residues: 265.7822 Evaluate side-chains 446 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 335 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1270 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 936 HIS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 0.0050 chunk 35 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1023 HIS J1218 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26773 Z= 0.295 Angle : 0.582 12.209 36442 Z= 0.296 Chirality : 0.042 0.181 4176 Planarity : 0.004 0.097 4545 Dihedral : 14.670 178.934 4360 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 5.40 % Allowed : 18.19 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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: -0.97 (0.15), residues: 3174 helix: 0.91 (0.16), residues: 1086 sheet: -1.28 (0.27), residues: 392 loop : -1.57 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J1193 HIS 0.007 0.001 HIS I1023 PHE 0.015 0.001 PHE H 8 TYR 0.017 0.001 TYR G 152 ARG 0.007 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 340 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9155 (mtmm) cc_final: 0.8819 (ptpp) REVERT: G 68 TYR cc_start: 0.9115 (m-80) cc_final: 0.8882 (m-10) REVERT: G 111 THR cc_start: 0.9150 (p) cc_final: 0.8884 (p) REVERT: G 202 VAL cc_start: 0.9478 (t) cc_final: 0.9240 (p) REVERT: H 79 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8586 (mm) REVERT: I 459 MET cc_start: 0.9042 (mtp) cc_final: 0.8466 (mtp) REVERT: I 463 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: I 488 MET cc_start: 0.8416 (mmp) cc_final: 0.7563 (tpt) REVERT: I 518 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8719 (p0) REVERT: I 930 ASP cc_start: 0.7297 (m-30) cc_final: 0.7089 (m-30) REVERT: I 997 TRP cc_start: 0.7284 (m100) cc_final: 0.6227 (m100) REVERT: I 1085 MET cc_start: 0.9118 (mmm) cc_final: 0.8800 (mmm) REVERT: I 1240 ASP cc_start: 0.8198 (p0) cc_final: 0.7897 (p0) REVERT: I 1265 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7676 (t80) REVERT: J 137 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8176 (mtp180) REVERT: J 180 MET cc_start: 0.7705 (ttm) cc_final: 0.7168 (ttm) REVERT: J 227 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8605 (m-80) REVERT: J 308 ASP cc_start: 0.8759 (t0) cc_final: 0.8311 (t0) REVERT: J 330 MET cc_start: 0.7928 (ptp) cc_final: 0.7608 (ptp) REVERT: J 560 ASN cc_start: 0.6725 (p0) cc_final: 0.6153 (p0) REVERT: J 644 MET cc_start: 0.8895 (mtt) cc_final: 0.8498 (mtt) REVERT: J 697 MET cc_start: 0.8705 (ttp) cc_final: 0.8320 (ttp) REVERT: J 698 MET cc_start: 0.7835 (tpt) cc_final: 0.6888 (tpt) REVERT: J 702 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.6538 (pp30) REVERT: J 802 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: J 806 ASP cc_start: 0.7732 (p0) cc_final: 0.7514 (p0) REVERT: J 822 MET cc_start: 0.8762 (mmt) cc_final: 0.8301 (mmt) REVERT: J 832 LYS cc_start: 0.7540 (mttt) cc_final: 0.7139 (mttp) REVERT: J 898 CYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7842 (m) REVERT: J 936 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6395 (m90) REVERT: J 1158 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6380 (tm-30) REVERT: J 1167 LYS cc_start: 0.6243 (tptp) cc_final: 0.5338 (mmmt) REVERT: K 31 GLN cc_start: 0.8962 (tt0) cc_final: 0.8697 (tt0) outliers start: 146 outliers final: 112 residues processed: 453 average time/residue: 0.3736 time to fit residues: 271.7028 Evaluate side-chains 450 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 329 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1178 LYS Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 936 HIS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1023 HIS J1218 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26773 Z= 0.278 Angle : 0.584 12.431 36442 Z= 0.295 Chirality : 0.042 0.189 4176 Planarity : 0.004 0.097 4545 Dihedral : 14.664 178.781 4358 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.43 % Allowed : 18.34 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3174 helix: 0.87 (0.16), residues: 1092 sheet: -1.26 (0.27), residues: 392 loop : -1.56 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.007 0.001 HIS I1023 PHE 0.014 0.001 PHE H 8 TYR 0.016 0.001 TYR G 152 ARG 0.008 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 342 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8823 (ptpp) REVERT: G 68 TYR cc_start: 0.9107 (m-80) cc_final: 0.8884 (m-10) REVERT: G 111 THR cc_start: 0.9141 (p) cc_final: 0.8880 (p) REVERT: G 202 VAL cc_start: 0.9476 (t) cc_final: 0.9265 (p) REVERT: H 79 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8598 (mm) REVERT: I 459 MET cc_start: 0.9043 (mtp) cc_final: 0.8475 (mtp) REVERT: I 463 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: I 488 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7531 (tpt) REVERT: I 518 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8697 (p0) REVERT: I 930 ASP cc_start: 0.7215 (m-30) cc_final: 0.7010 (m-30) REVERT: I 997 TRP cc_start: 0.7411 (m100) cc_final: 0.6344 (m100) REVERT: I 1085 MET cc_start: 0.9118 (mmm) cc_final: 0.8803 (mmm) REVERT: I 1240 ASP cc_start: 0.8209 (p0) cc_final: 0.7897 (p0) REVERT: I 1265 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7718 (t80) REVERT: J 137 ARG cc_start: 0.8499 (mtp180) cc_final: 0.8289 (mtp180) REVERT: J 227 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8605 (m-80) REVERT: J 308 ASP cc_start: 0.8755 (t0) cc_final: 0.8339 (t0) REVERT: J 330 MET cc_start: 0.7903 (ptp) cc_final: 0.7561 (ptp) REVERT: J 560 ASN cc_start: 0.6728 (p0) cc_final: 0.6135 (p0) REVERT: J 643 ASP cc_start: 0.8740 (m-30) cc_final: 0.8441 (m-30) REVERT: J 644 MET cc_start: 0.8890 (mtt) cc_final: 0.8507 (mtt) REVERT: J 697 MET cc_start: 0.8688 (ttp) cc_final: 0.8292 (ttp) REVERT: J 698 MET cc_start: 0.7821 (tpt) cc_final: 0.6867 (tpt) REVERT: J 702 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.6420 (pp30) REVERT: J 783 LEU cc_start: 0.9424 (mt) cc_final: 0.8993 (mp) REVERT: J 802 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: J 806 ASP cc_start: 0.7727 (p0) cc_final: 0.7514 (p0) REVERT: J 822 MET cc_start: 0.8764 (mmt) cc_final: 0.8300 (mmt) REVERT: J 832 LYS cc_start: 0.7487 (mttt) cc_final: 0.7062 (mttp) REVERT: J 898 CYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7842 (m) REVERT: J 925 GLU cc_start: 0.8522 (pp20) cc_final: 0.8302 (pp20) REVERT: J 936 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6419 (m90) REVERT: J 1158 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6375 (tm-30) REVERT: K 31 GLN cc_start: 0.8953 (tt0) cc_final: 0.8680 (tt0) outliers start: 147 outliers final: 117 residues processed: 457 average time/residue: 0.3644 time to fit residues: 268.1054 Evaluate side-chains 458 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 331 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1247 SER Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 936 HIS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 288 optimal weight: 30.0000 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 260 optimal weight: 0.0980 chunk 272 optimal weight: 20.0000 chunk 287 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: I1023 HIS J1218 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26773 Z= 0.207 Angle : 0.563 12.650 36442 Z= 0.284 Chirality : 0.042 0.251 4176 Planarity : 0.004 0.095 4545 Dihedral : 14.623 178.108 4358 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.77 % Allowed : 18.82 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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: -0.88 (0.15), residues: 3174 helix: 0.98 (0.16), residues: 1089 sheet: -1.17 (0.27), residues: 390 loop : -1.52 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.008 0.001 HIS I1023 PHE 0.013 0.001 PHE H 8 TYR 0.015 0.001 TYR G 152 ARG 0.007 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 352 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9131 (mtmm) cc_final: 0.8829 (ptpp) REVERT: G 68 TYR cc_start: 0.9067 (m-80) cc_final: 0.8833 (m-10) REVERT: G 111 THR cc_start: 0.9127 (p) cc_final: 0.8865 (p) REVERT: G 202 VAL cc_start: 0.9461 (t) cc_final: 0.9214 (p) REVERT: H 79 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8364 (mm) REVERT: I 459 MET cc_start: 0.9023 (mtp) cc_final: 0.8492 (mtp) REVERT: I 463 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: I 488 MET cc_start: 0.8353 (mmp) cc_final: 0.7381 (tpt) REVERT: I 518 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8571 (p0) REVERT: I 997 TRP cc_start: 0.7435 (m-10) cc_final: 0.6333 (m100) REVERT: I 1085 MET cc_start: 0.9098 (mmm) cc_final: 0.8791 (mmm) REVERT: I 1240 ASP cc_start: 0.8204 (p0) cc_final: 0.7884 (p0) REVERT: I 1265 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7537 (t80) REVERT: I 1321 GLU cc_start: 0.7707 (mp0) cc_final: 0.7452 (mp0) REVERT: J 137 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8112 (mtp180) REVERT: J 180 MET cc_start: 0.7734 (ttm) cc_final: 0.7108 (ttm) REVERT: J 227 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: J 308 ASP cc_start: 0.8748 (t0) cc_final: 0.8360 (t0) REVERT: J 560 ASN cc_start: 0.6745 (p0) cc_final: 0.6137 (p0) REVERT: J 643 ASP cc_start: 0.8726 (m-30) cc_final: 0.8413 (m-30) REVERT: J 644 MET cc_start: 0.8847 (mtt) cc_final: 0.8457 (mtt) REVERT: J 697 MET cc_start: 0.8653 (ttp) cc_final: 0.8241 (ttp) REVERT: J 698 MET cc_start: 0.7820 (tpt) cc_final: 0.6878 (tpt) REVERT: J 702 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.6359 (pp30) REVERT: J 802 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: J 806 ASP cc_start: 0.7705 (p0) cc_final: 0.7495 (p0) REVERT: J 822 MET cc_start: 0.8859 (mmt) cc_final: 0.8385 (mmt) REVERT: J 832 LYS cc_start: 0.7430 (mttt) cc_final: 0.7004 (mttp) REVERT: J 898 CYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7791 (m) REVERT: J 925 GLU cc_start: 0.8494 (pp20) cc_final: 0.8270 (pp20) REVERT: J 936 HIS cc_start: 0.6932 (OUTLIER) cc_final: 0.6220 (m90) REVERT: J 1158 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6311 (tm-30) REVERT: K 31 GLN cc_start: 0.8940 (tt0) cc_final: 0.8650 (tt0) outliers start: 129 outliers final: 108 residues processed: 447 average time/residue: 0.3670 time to fit residues: 264.5077 Evaluate side-chains 451 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 334 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 936 HIS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 3.9990 chunk 304 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 chunk 211 optimal weight: 4.9990 chunk 319 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 737 ASN I1023 HIS J1098 GLN J1218 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26773 Z= 0.214 Angle : 0.571 12.928 36442 Z= 0.287 Chirality : 0.042 0.201 4176 Planarity : 0.004 0.094 4545 Dihedral : 14.608 178.201 4353 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.70 % Allowed : 19.00 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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: -0.89 (0.15), residues: 3174 helix: 0.95 (0.16), residues: 1095 sheet: -1.18 (0.27), residues: 391 loop : -1.53 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.008 0.001 HIS I1023 PHE 0.012 0.001 PHE H 8 TYR 0.015 0.001 TYR G 152 ARG 0.007 0.000 ARG I 779 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 345 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8857 (ptpp) REVERT: G 68 TYR cc_start: 0.9083 (m-80) cc_final: 0.8846 (m-10) REVERT: G 111 THR cc_start: 0.9129 (p) cc_final: 0.8865 (p) REVERT: G 202 VAL cc_start: 0.9459 (t) cc_final: 0.9209 (p) REVERT: H 79 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8364 (mm) REVERT: H 95 LYS cc_start: 0.6990 (mtpt) cc_final: 0.6776 (mtpt) REVERT: I 459 MET cc_start: 0.9025 (mtp) cc_final: 0.8507 (mtp) REVERT: I 463 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: I 488 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7396 (tpt) REVERT: I 518 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8517 (p0) REVERT: I 737 ASN cc_start: 0.8059 (m110) cc_final: 0.7703 (m-40) REVERT: I 997 TRP cc_start: 0.7529 (m-10) cc_final: 0.6438 (m100) REVERT: I 1085 MET cc_start: 0.9099 (mmm) cc_final: 0.8783 (mmm) REVERT: I 1107 MET cc_start: 0.7985 (mtm) cc_final: 0.7761 (mtm) REVERT: I 1240 ASP cc_start: 0.8198 (p0) cc_final: 0.7877 (p0) REVERT: I 1265 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7678 (t80) REVERT: I 1321 GLU cc_start: 0.7703 (mp0) cc_final: 0.7442 (mp0) REVERT: J 137 ARG cc_start: 0.8483 (mtp180) cc_final: 0.8064 (mtp180) REVERT: J 227 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: J 308 ASP cc_start: 0.8755 (t0) cc_final: 0.8341 (t0) REVERT: J 560 ASN cc_start: 0.6767 (p0) cc_final: 0.6187 (p0) REVERT: J 643 ASP cc_start: 0.8735 (m-30) cc_final: 0.8419 (m-30) REVERT: J 644 MET cc_start: 0.8852 (mtt) cc_final: 0.8463 (mtt) REVERT: J 697 MET cc_start: 0.8659 (ttp) cc_final: 0.8253 (ttp) REVERT: J 698 MET cc_start: 0.7828 (tpt) cc_final: 0.6901 (tpt) REVERT: J 702 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.6430 (pp30) REVERT: J 802 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: J 822 MET cc_start: 0.8778 (mmt) cc_final: 0.8275 (mmt) REVERT: J 832 LYS cc_start: 0.7387 (mttt) cc_final: 0.6927 (mttp) REVERT: J 898 CYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7771 (m) REVERT: J 925 GLU cc_start: 0.8499 (pp20) cc_final: 0.8264 (pp20) REVERT: J 936 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6223 (m90) REVERT: J 1158 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6297 (tm-30) REVERT: J 1283 SER cc_start: 0.8949 (m) cc_final: 0.8685 (p) REVERT: K 31 GLN cc_start: 0.8943 (tt0) cc_final: 0.8670 (tt0) outliers start: 127 outliers final: 107 residues processed: 441 average time/residue: 0.3853 time to fit residues: 274.0278 Evaluate side-chains 453 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 336 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 999 GLU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1101 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 936 HIS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1045 THR Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 2.9990 chunk 271 optimal weight: 30.0000 chunk 78 optimal weight: 0.0370 chunk 234 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1023 HIS J1218 HIS ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.096888 restraints weight = 42539.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.096554 restraints weight = 30937.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.097482 restraints weight = 25631.360| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26773 Z= 0.194 Angle : 0.571 15.113 36442 Z= 0.285 Chirality : 0.042 0.206 4176 Planarity : 0.004 0.094 4545 Dihedral : 14.578 177.951 4350 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.58 % Allowed : 19.48 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % 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: -0.81 (0.15), residues: 3174 helix: 1.04 (0.16), residues: 1088 sheet: -1.08 (0.27), residues: 398 loop : -1.50 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J1193 HIS 0.008 0.001 HIS I1023 PHE 0.011 0.001 PHE H 8 TYR 0.015 0.001 TYR G 152 ARG 0.007 0.000 ARG I 779 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5510.99 seconds wall clock time: 103 minutes 52.72 seconds (6232.72 seconds total)