Starting phenix.real_space_refine on Sat Aug 8 08:51:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10me_75283/08_2026/10me_75283.cif Found real_map, /net/cci-nas-00/data/ceres_data/10me_75283/08_2026/10me_75283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10me_75283/08_2026/10me_75283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10me_75283/08_2026/10me_75283.map" model { file = "/net/cci-nas-00/data/ceres_data/10me_75283/08_2026/10me_75283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10me_75283/08_2026/10me_75283.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.004 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 16257 2.51 5 N 4640 2.21 5 O 5177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26246 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: "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: {'PTRANS': 8, '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: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10375 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} 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: "J" Number of atoms: 10533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10533 Classifications: {'peptide': 1358} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 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: 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: "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} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15291 SG CYS J 70 115.326 54.556 68.076 1.00380.13 S ATOM 15305 SG CYS J 72 115.829 50.979 66.818 1.00364.59 S ATOM 15413 SG CYS J 85 116.551 52.514 64.975 1.00389.88 S ATOM 15437 SG CYS J 88 113.506 53.406 64.862 1.00388.67 S ATOM 21117 SG CYS J 814 88.181 117.622 67.350 1.00269.74 S ATOM 21682 SG CYS J 888 85.673 114.558 68.088 1.00269.87 S ATOM 21733 SG CYS J 895 87.583 116.796 71.344 1.00262.27 S ATOM 21754 SG CYS J 898 84.629 116.810 69.223 1.00278.35 S Time building chain proxies: 6.15, per 1000 atoms: 0.23 Number of scatterers: 26246 At special positions: 0 Unit cell: (142.636, 156.832, 162.916, 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 5177 8.00 N 4640 7.00 C 16257 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 - 3.00 Amino acid : True - 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " 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... Secondary structure from input PDB file: 113 helices and 49 sheets defined 39.7% alpha, 15.9% beta 25 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.688A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 removed outlier: 4.203A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.655A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.543A pdb=" N THR H 157 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 229 removed outlier: 3.657A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.605A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.513A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.846A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.020A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 289 through 293 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 353 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 391 removed outlier: 4.055A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER I 391 " --> pdb=" O ASN I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 410 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.676A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 539 through 543 Processing helix chain 'I' and resid 607 through 612 removed outlier: 3.722A pdb=" N GLU I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 607 through 612' Processing helix chain 'I' and resid 662 through 667 removed outlier: 3.922A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 removed outlier: 3.503A pdb=" N HIS I 673 " --> pdb=" O PHE I 670 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 703 through 712 removed outlier: 4.508A pdb=" N ALA I 707 " --> pdb=" O GLY I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.624A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 removed outlier: 3.500A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY I 982 " --> pdb=" O VAL I 978 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY I 983 " --> pdb=" O LEU I 979 " (cutoff:3.500A) Processing helix chain 'I' and resid 984 through 992 removed outlier: 3.978A pdb=" N LYS I 988 " --> pdb=" O VAL I 984 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.190A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.813A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1284 through 1293 removed outlier: 3.612A pdb=" N VAL I1293 " --> pdb=" O GLU I1289 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.555A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1334 removed outlier: 3.741A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY I1334 " --> pdb=" O ILE I1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.523A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.742A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 167 Processing helix chain 'J' and resid 168 through 173 removed outlier: 4.121A pdb=" N PHE J 172 " --> pdb=" O ALA J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 176 No H-bonds generated for 'chain 'J' and resid 174 through 176' Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.767A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.735A pdb=" N LYS J 216 " --> pdb=" O THR J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 318 through 322 removed outlier: 3.646A pdb=" N ARG J 322 " --> pdb=" O SER J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.797A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.832A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 419 No H-bonds generated for 'chain 'J' and resid 417 through 419' Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 removed outlier: 3.638A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.704A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.776A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.581A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER J 635 " --> pdb=" O TYR J 631 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.011A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 725 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 789 removed outlier: 3.585A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 804 Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 932 removed outlier: 4.159A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Proline residue: J 926 - end of helix removed outlier: 3.722A pdb=" N MET J 932 " --> pdb=" O THR J 928 " (cutoff:3.500A) Processing helix chain 'J' and resid 933 through 937 removed outlier: 3.512A pdb=" N HIS J 936 " --> pdb=" O ARG J 933 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE J 937 " --> pdb=" O THR J 934 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 933 through 937' Processing helix chain 'J' and resid 1133 through 1146 removed outlier: 3.779A pdb=" N LEU J1138 " --> pdb=" O ILE J1134 " (cutoff:3.500A) Proline residue: J1139 - end of helix Processing helix chain 'J' and resid 1168 through 1170 No H-bonds generated for 'chain 'J' and resid 1168 through 1170' Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.761A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR J1241 " --> pdb=" O VAL J1237 " (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 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.693A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.940A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 15 through 33 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 removed outlier: 4.090A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.936A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 6.057A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL G 59 " --> pdb=" O LEU G 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 108 through 111 removed outlier: 4.262A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA5, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.938A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 98 through 105 removed outlier: 5.842A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AA8, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.532A pdb=" N VAL H 153 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA H 175 " --> pdb=" O VAL H 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.973A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLU I 106 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL I 114 " --> pdb=" O GLU I 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 143 through 145 Processing sheet with id=AB2, first strand: chain 'I' and resid 148 through 151 Processing sheet with id=AB3, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.679A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 284 through 286 removed outlier: 5.843A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.652A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'I' and resid 529 through 530 Processing sheet with id=AB8, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.872A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.872A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'I' and resid 700 through 701 Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.980A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.087A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.527A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE I 765 " --> pdb=" O THR I 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1076 through 1080 removed outlier: 7.394A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE I 804 " --> pdb=" O THR I1226 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 832 Processing sheet with id=AC9, first strand: chain 'I' and resid 835 through 841 removed outlier: 3.515A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 876 through 877 removed outlier: 3.513A pdb=" N GLY I 926 " --> pdb=" O VAL I 877 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.778A pdb=" N HIS I1244 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.621A pdb=" N ILE J 20 " --> pdb=" O ASP J1342 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP J1342 " --> pdb=" O ILE J 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 103 through 112 removed outlier: 3.684A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU J 107 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD7, first strand: chain 'J' and resid 355 through 356 Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 removed outlier: 7.415A pdb=" N LEU J 527 " --> pdb=" O ARG J 551 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N THR J 553 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP J 558 " --> pdb=" O GLU J 562 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU J 562 " --> pdb=" O ASP J 558 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 removed outlier: 3.549A pdb=" N THR J 810 " --> pdb=" O VAL J 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.701A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 848 through 849 removed outlier: 7.025A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.122A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 991 through 997 removed outlier: 6.901A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS J 996 " --> pdb=" O THR J 980 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR J 980 " --> pdb=" O LYS J 996 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE8, first strand: chain 'J' and resid 1025 through 1028 removed outlier: 3.832A pdb=" N MET J1025 " --> pdb=" O ILE J1124 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1098 through 1099 Processing sheet with id=AF1, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.853A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1155 through 1156 Processing sheet with id=AF3, first strand: chain 'J' and resid 1188 through 1191 Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 1038 hydrogen bonds defined for protein. 2907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 6.19 Time building geometry restraints manager: 3.21 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: 8731 1.34 - 1.46: 4730 1.46 - 1.58: 13001 1.58 - 1.70: 123 1.70 - 1.82: 184 Bond restraints: 26769 Sorted by residual: bond pdb=" C3' DA B 29 " pdb=" C2' DA B 29 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DA A 21 " pdb=" C2' DA A 21 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.85e+00 bond pdb=" C1' DT B 4 " pdb=" N1 DT B 4 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.85e+00 bond pdb=" C1' DC A 6 " pdb=" N1 DC A 6 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.79e+00 bond pdb=" C1' DC B 11 " pdb=" N1 DC B 11 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.40e+00 ... (remaining 26764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 35072 1.17 - 2.34: 1069 2.34 - 3.52: 249 3.52 - 4.69: 44 4.69 - 5.86: 3 Bond angle restraints: 36437 Sorted by residual: angle pdb=" O4' DC B 18 " pdb=" C4' DC B 18 " pdb=" C3' DC B 18 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.83e+01 angle pdb=" N3 DT B 24 " pdb=" C4 DT B 24 " pdb=" O4 DT B 24 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT A 26 " pdb=" C4 DT A 26 " pdb=" O4 DT A 26 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" O4' DC B 20 " pdb=" C4' DC B 20 " pdb=" C3' DC B 20 " ideal model delta sigma weight residual 106.00 103.47 2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" O4 DT B 24 " pdb=" C4 DT B 24 " pdb=" C5 DT B 24 " ideal model delta sigma weight residual 124.90 121.96 2.94 7.00e-01 2.04e+00 1.77e+01 ... (remaining 36432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 16054 35.32 - 70.64: 339 70.64 - 105.96: 5 105.96 - 141.28: 0 141.28 - 176.60: 1 Dihedral angle restraints: 16399 sinusoidal: 7248 harmonic: 9151 Sorted by residual: dihedral pdb=" CA CYS J 814 " pdb=" C CYS J 814 " pdb=" N GLY J 815 " pdb=" CA GLY J 815 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLY J 815 " pdb=" C GLY J 815 " pdb=" N THR J 816 " pdb=" CA THR J 816 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" C4' DG A 24 " pdb=" C3' DG A 24 " pdb=" O3' DG A 24 " pdb=" P DA A 25 " ideal model delta sinusoidal sigma weight residual 220.00 43.40 176.60 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 16396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3434 0.049 - 0.098: 519 0.098 - 0.147: 201 0.147 - 0.195: 21 0.195 - 0.244: 1 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C1' G R 17 " pdb=" O4' G R 17 " pdb=" C2' G R 17 " pdb=" N9 G R 17 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' DG B 17 " pdb=" C4' DG B 17 " pdb=" O3' DG B 17 " pdb=" C2' DG B 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" C3' DC B 20 " pdb=" C4' DC B 20 " pdb=" O3' DC B 20 " pdb=" C2' DC B 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 4173 not shown) Planarity restraints: 4544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G R 17 " -0.025 2.00e-02 2.50e+03 1.30e-02 5.06e+00 pdb=" N9 G R 17 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G R 17 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G R 17 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G R 17 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G R 17 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G R 17 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G R 17 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G R 17 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G R 17 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G R 17 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G R 17 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS I 559 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO I 560 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 560 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 560 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C R 18 " -0.028 2.00e-02 2.50e+03 1.39e-02 4.33e+00 pdb=" N1 C R 18 " 0.027 2.00e-02 2.50e+03 pdb=" C2 C R 18 " 0.010 2.00e-02 2.50e+03 pdb=" O2 C R 18 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C R 18 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C R 18 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C R 18 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C R 18 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C R 18 " 0.006 2.00e-02 2.50e+03 ... (remaining 4541 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 5 2.34 - 2.98: 15041 2.98 - 3.62: 39515 3.62 - 4.26: 57849 4.26 - 4.90: 94588 Nonbonded interactions: 206998 Sorted by model distance: nonbonded pdb=" OP1 U R 19 " pdb="MG MG R1501 " model vdw 1.704 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG R1501 " model vdw 1.907 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG R1501 " model vdw 2.251 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG R1501 " model vdw 2.288 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG R1501 " model vdw 2.290 2.170 ... (remaining 206993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 4.440 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: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.970 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.004 0.223 26777 Z= 0.234 Angle : 0.647 42.349 36449 Z= 0.348 Chirality : 0.042 0.244 4176 Planarity : 0.004 0.054 4544 Dihedral : 12.916 176.597 10515 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.81 % Allowed : 6.73 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3174 helix: 1.20 (0.16), residues: 1114 sheet: -0.30 (0.26), residues: 417 loop : -0.60 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1216 TYR 0.017 0.001 TYR J 772 PHE 0.012 0.001 PHE I1270 TRP 0.008 0.001 TRP J1193 HIS 0.004 0.001 HIS J1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.22 (26769) covalent geometry : angle 0.52509 / 0.34 (36437) hydrogen bonds : bond 0.12788 / 14.04 ( 1101) hydrogen bonds : angle 6.27353 / 6.50 ( 3035) metal coordination : bond 0.12426 / 13.10 ( 8) metal coordination : angle 20.79899 / 37.84 ( 12) *********************** 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 648 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 545 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8928 (m-80) cc_final: 0.8681 (m-80) REVERT: G 51 MET cc_start: 0.9276 (mmm) cc_final: 0.8882 (mmm) REVERT: G 84 ASN cc_start: 0.9082 (m110) cc_final: 0.8510 (m-40) REVERT: G 105 SER cc_start: 0.8029 (p) cc_final: 0.7788 (p) REVERT: G 177 TYR cc_start: 0.8184 (m-80) cc_final: 0.7578 (m-80) REVERT: G 199 ASP cc_start: 0.9216 (m-30) cc_final: 0.8879 (m-30) REVERT: H 9 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8187 (tp) REVERT: H 10 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8690 (mmmt) REVERT: H 35 PHE cc_start: 0.9124 (m-80) cc_final: 0.8138 (m-80) REVERT: H 146 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8615 (t) REVERT: H 147 GLN cc_start: 0.9214 (tt0) cc_final: 0.8739 (tp-100) REVERT: H 191 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.9038 (ptm-80) REVERT: H 203 ILE cc_start: 0.9331 (mt) cc_final: 0.9093 (mp) REVERT: I 23 ASP cc_start: 0.9350 (p0) cc_final: 0.9137 (t70) REVERT: I 85 CYS cc_start: 0.9332 (m) cc_final: 0.9089 (m) REVERT: I 213 LEU cc_start: 0.9304 (mt) cc_final: 0.9102 (mt) REVERT: I 389 PHE cc_start: 0.9675 (m-80) cc_final: 0.9371 (m-80) REVERT: I 459 MET cc_start: 0.8311 (mtp) cc_final: 0.7950 (mtm) REVERT: I 538 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7456 (pp) REVERT: I 565 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7833 (pm20) REVERT: I 641 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9136 (mp0) REVERT: I 653 MET cc_start: 0.8870 (ttt) cc_final: 0.8481 (tmm) REVERT: I 733 VAL cc_start: 0.8823 (t) cc_final: 0.8578 (p) REVERT: I 742 TYR cc_start: 0.9207 (m-80) cc_final: 0.8815 (m-80) REVERT: I 758 ARG cc_start: 0.8803 (ttt-90) cc_final: 0.8601 (ttt90) REVERT: I 789 THR cc_start: 0.9120 (m) cc_final: 0.8877 (p) REVERT: I 829 THR cc_start: 0.9291 (m) cc_final: 0.8884 (p) REVERT: I 833 ILE cc_start: 0.8515 (mt) cc_final: 0.8094 (mp) REVERT: I 930 ASP cc_start: 0.8855 (t0) cc_final: 0.8189 (t0) REVERT: I 936 ARG cc_start: 0.8964 (ttm-80) cc_final: 0.8592 (tpp-160) REVERT: I 964 LEU cc_start: 0.9669 (tp) cc_final: 0.9421 (tp) REVERT: I 1080 ASN cc_start: 0.9068 (t0) cc_final: 0.8591 (t0) REVERT: I 1092 THR cc_start: 0.8732 (m) cc_final: 0.8223 (p) REVERT: I 1131 MET cc_start: 0.9543 (mtp) cc_final: 0.9135 (mtp) REVERT: I 1170 MET cc_start: 0.9771 (mmm) cc_final: 0.9526 (mmm) REVERT: I 1180 MET cc_start: 0.8908 (ttm) cc_final: 0.8379 (ttt) REVERT: I 1251 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: I 1290 MET cc_start: 0.8930 (mmt) cc_final: 0.8719 (tpp) REVERT: J 107 LEU cc_start: 0.9033 (mt) cc_final: 0.8544 (mt) REVERT: J 242 LEU cc_start: 0.9506 (tp) cc_final: 0.9212 (pp) REVERT: J 245 LEU cc_start: 0.9634 (tp) cc_final: 0.9419 (tt) REVERT: J 340 GLN cc_start: 0.8775 (tp40) cc_final: 0.8105 (mm110) REVERT: J 491 LEU cc_start: 0.8685 (mt) cc_final: 0.8341 (tt) REVERT: J 521 LYS cc_start: 0.9529 (tptm) cc_final: 0.9326 (tttm) REVERT: J 686 TRP cc_start: 0.9541 (m100) cc_final: 0.8768 (m100) REVERT: J 697 MET cc_start: 0.8994 (pp-130) cc_final: 0.8775 (tmm) REVERT: J 707 ILE cc_start: 0.9388 (tt) cc_final: 0.9075 (mp) REVERT: J 739 GLN cc_start: 0.8447 (mt0) cc_final: 0.8201 (mt0) REVERT: J 743 MET cc_start: 0.8868 (ttp) cc_final: 0.8617 (ttm) REVERT: J 747 MET cc_start: 0.7924 (mpt) cc_final: 0.6575 (tpt) REVERT: J 788 LEU cc_start: 0.9456 (mm) cc_final: 0.9254 (mm) REVERT: J 932 MET cc_start: 0.7995 (mtm) cc_final: 0.7316 (mmt) REVERT: J 1219 ASP cc_start: 0.9612 (m-30) cc_final: 0.9341 (p0) REVERT: J 1284 ARG cc_start: 0.9672 (mtp180) cc_final: 0.9423 (ttm110) REVERT: K 12 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8665 (mmmt) REVERT: K 43 ASN cc_start: 0.9033 (t0) cc_final: 0.8814 (t0) REVERT: K 48 VAL cc_start: 0.9313 (t) cc_final: 0.9092 (t) REVERT: K 49 ILE cc_start: 0.9686 (mt) cc_final: 0.9322 (mm) REVERT: K 51 LEU cc_start: 0.9725 (mt) cc_final: 0.9475 (tp) REVERT: K 52 ARG cc_start: 0.9524 (mtp180) cc_final: 0.9084 (mtp180) REVERT: K 58 LEU cc_start: 0.9542 (pt) cc_final: 0.9142 (pt) outliers start: 103 outliers final: 52 residues processed: 633 average time/residue: 0.2012 time to fit residues: 194.9375 Evaluate side-chains 384 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 327 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 674 ASP Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 815 SER Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 995 ASP Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1251 TYR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 0.0070 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 40.0000 chunk 298 optimal weight: 20.0000 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN I 510 GLN I 677 ASN I 932 GLN I1010 GLN J 875 ASN ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.098255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063744 restraints weight = 102842.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.066136 restraints weight = 58221.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066445 restraints weight = 34445.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.066576 restraints weight = 34559.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.066693 restraints weight = 32180.574| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26777 Z= 0.146 Angle : 0.704 26.695 36449 Z= 0.348 Chirality : 0.045 0.242 4176 Planarity : 0.005 0.093 4544 Dihedral : 13.826 178.071 4412 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.55 % Allowed : 14.02 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3174 helix: 1.44 (0.15), residues: 1114 sheet: -0.09 (0.26), residues: 405 loop : -0.48 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 195 TYR 0.023 0.001 TYR J 679 PHE 0.023 0.002 PHE I 389 TRP 0.022 0.002 TRP I 997 HIS 0.008 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (26769) covalent geometry : angle 0.66117 / 0.34 (36437) hydrogen bonds : bond 0.04865 / 5.34 ( 1101) hydrogen bonds : angle 5.12150 / 5.37 ( 3035) metal coordination : bond 0.01009 / 1.10 ( 8) metal coordination : angle 13.37674 / 22.80 ( 12) *********************** 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 476 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 380 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 49 SER cc_start: 0.9108 (p) cc_final: 0.8762 (p) REVERT: G 84 ASN cc_start: 0.8540 (m110) cc_final: 0.8331 (m-40) REVERT: G 177 TYR cc_start: 0.7862 (m-80) cc_final: 0.7421 (m-80) REVERT: H 9 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8620 (tp) REVERT: H 35 PHE cc_start: 0.8843 (m-80) cc_final: 0.7730 (m-80) REVERT: H 51 MET cc_start: 0.8157 (mmm) cc_final: 0.7752 (mmm) REVERT: H 205 MET cc_start: 0.8752 (tpp) cc_final: 0.8254 (tpt) REVERT: I 100 LEU cc_start: 0.9111 (mt) cc_final: 0.8668 (tp) REVERT: I 403 MET cc_start: 0.9057 (tmm) cc_final: 0.8726 (tmm) REVERT: I 404 LYS cc_start: 0.9580 (mmmt) cc_final: 0.9329 (mmmt) REVERT: I 538 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7525 (pp) REVERT: I 742 TYR cc_start: 0.8910 (m-80) cc_final: 0.8671 (m-80) REVERT: I 819 SER cc_start: 0.9034 (t) cc_final: 0.8831 (m) REVERT: I 829 THR cc_start: 0.9238 (m) cc_final: 0.8913 (p) REVERT: I 836 LEU cc_start: 0.8865 (mm) cc_final: 0.8631 (mm) REVERT: I 876 GLU cc_start: 0.8547 (tp30) cc_final: 0.8027 (tm-30) REVERT: I 930 ASP cc_start: 0.8344 (t0) cc_final: 0.8143 (t0) REVERT: I 936 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8507 (tpp-160) REVERT: I 1092 THR cc_start: 0.8982 (m) cc_final: 0.8525 (p) REVERT: I 1131 MET cc_start: 0.8859 (mtp) cc_final: 0.8571 (mtp) REVERT: I 1180 MET cc_start: 0.8960 (ttm) cc_final: 0.8733 (ttt) REVERT: I 1251 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: J 128 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9229 (tp) REVERT: J 224 LEU cc_start: 0.9738 (mt) cc_final: 0.9480 (pp) REVERT: J 245 LEU cc_start: 0.9629 (tp) cc_final: 0.9340 (tt) REVERT: J 340 GLN cc_start: 0.8583 (tp40) cc_final: 0.7963 (mm110) REVERT: J 649 LYS cc_start: 0.9649 (OUTLIER) cc_final: 0.8848 (tptt) REVERT: J 686 TRP cc_start: 0.9019 (m100) cc_final: 0.8521 (m100) REVERT: J 697 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8054 (tmm) REVERT: J 724 MET cc_start: 0.8934 (mtm) cc_final: 0.8700 (mtm) REVERT: J 747 MET cc_start: 0.7464 (mpt) cc_final: 0.7157 (mmm) REVERT: J 1190 ILE cc_start: 0.9450 (pt) cc_final: 0.9034 (mp) REVERT: K 48 VAL cc_start: 0.9315 (t) cc_final: 0.8989 (t) REVERT: K 49 ILE cc_start: 0.9730 (mt) cc_final: 0.9240 (mm) REVERT: K 52 ARG cc_start: 0.9484 (mtp180) cc_final: 0.9002 (ptm160) outliers start: 96 outliers final: 56 residues processed: 454 average time/residue: 0.1887 time to fit residues: 134.5561 Evaluate side-chains 367 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 305 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1251 TYR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1279 GLN Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 288 optimal weight: 40.0000 chunk 187 optimal weight: 20.0000 chunk 268 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 147 GLN H 194 GLN I1090 ASN J 495 ASN J 929 GLN ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.096950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.065622 restraints weight = 104802.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065118 restraints weight = 63068.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.065680 restraints weight = 47856.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065974 restraints weight = 42223.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066109 restraints weight = 38852.514| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26777 Z= 0.161 Angle : 0.678 22.052 36449 Z= 0.338 Chirality : 0.044 0.349 4176 Planarity : 0.004 0.058 4544 Dihedral : 13.766 176.306 4379 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.40 % Allowed : 14.98 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3174 helix: 1.38 (0.15), residues: 1118 sheet: -0.33 (0.25), residues: 436 loop : -0.53 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 67 TYR 0.066 0.001 TYR J 679 PHE 0.013 0.001 PHE J1165 TRP 0.014 0.001 TRP I 997 HIS 0.010 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (26769) covalent geometry : angle 0.64522 / 0.34 (36437) hydrogen bonds : bond 0.04566 / 4.99 ( 1101) hydrogen bonds : angle 5.08358 / 5.39 ( 3035) metal coordination : bond 0.00816 / 0.89 ( 8) metal coordination : angle 11.49806 / 19.42 ( 12) *********************** 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 438 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 319 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7763 (ptpp) cc_final: 0.7561 (ptpp) REVERT: G 177 TYR cc_start: 0.7928 (m-80) cc_final: 0.7508 (m-80) REVERT: G 205 MET cc_start: 0.8245 (tmm) cc_final: 0.7887 (tmm) REVERT: H 9 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8575 (tp) REVERT: H 35 PHE cc_start: 0.8828 (m-80) cc_final: 0.7731 (m-80) REVERT: H 51 MET cc_start: 0.8320 (mmm) cc_final: 0.7865 (mmm) REVERT: H 152 TYR cc_start: 0.8314 (t80) cc_final: 0.8072 (t80) REVERT: I 100 LEU cc_start: 0.8981 (mt) cc_final: 0.8600 (tp) REVERT: I 365 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.9029 (mp0) REVERT: I 538 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7473 (pp) REVERT: I 653 MET cc_start: 0.8199 (tmm) cc_final: 0.7796 (tmm) REVERT: I 775 GLU cc_start: 0.8376 (tt0) cc_final: 0.8127 (tt0) REVERT: I 829 THR cc_start: 0.9247 (m) cc_final: 0.8946 (p) REVERT: I 876 GLU cc_start: 0.8481 (tp30) cc_final: 0.8146 (tp30) REVERT: I 995 ASP cc_start: 0.9276 (OUTLIER) cc_final: 0.8929 (p0) REVERT: I 998 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8414 (mm) REVERT: I 1025 PHE cc_start: 0.9012 (m-80) cc_final: 0.8808 (m-80) REVERT: I 1092 THR cc_start: 0.8914 (m) cc_final: 0.8441 (p) REVERT: I 1131 MET cc_start: 0.8937 (mtp) cc_final: 0.8646 (mtp) REVERT: I 1180 MET cc_start: 0.8963 (ttm) cc_final: 0.8723 (ttt) REVERT: I 1251 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: I 1304 MET cc_start: 0.9004 (ttp) cc_final: 0.8707 (ptm) REVERT: J 128 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.8998 (tp) REVERT: J 130 MET cc_start: 0.8797 (mmm) cc_final: 0.8221 (mmm) REVERT: J 160 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8760 (mm) REVERT: J 224 LEU cc_start: 0.9735 (mt) cc_final: 0.9491 (pp) REVERT: J 340 GLN cc_start: 0.8628 (tp40) cc_final: 0.7959 (mm110) REVERT: J 495 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8829 (p0) REVERT: J 679 TYR cc_start: 0.9279 (p90) cc_final: 0.9010 (p90) REVERT: J 686 TRP cc_start: 0.8998 (m100) cc_final: 0.8508 (m100) REVERT: J 697 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8143 (tmm) REVERT: J 747 MET cc_start: 0.7553 (mpt) cc_final: 0.7217 (mmm) REVERT: J 935 PHE cc_start: 0.8487 (p90) cc_final: 0.8176 (p90) REVERT: J 1040 MET cc_start: 0.5941 (mtt) cc_final: 0.4100 (mpp) REVERT: J 1189 MET cc_start: 0.9172 (tpp) cc_final: 0.8700 (tpp) REVERT: J 1190 ILE cc_start: 0.9384 (pt) cc_final: 0.8881 (mp) REVERT: K 8 ASP cc_start: 0.9198 (t0) cc_final: 0.8578 (t0) REVERT: K 12 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8872 (mmmt) REVERT: K 52 ARG cc_start: 0.9479 (mtp180) cc_final: 0.9213 (mtp180) outliers start: 119 outliers final: 84 residues processed: 403 average time/residue: 0.1707 time to fit residues: 110.0416 Evaluate side-chains 382 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 288 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 952 GLN Chi-restraints excluded: chain I residue 995 ASP Chi-restraints excluded: chain I residue 997 TRP Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1251 TYR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1279 GLN Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 208 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 227 optimal weight: 0.1980 chunk 160 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 37 HIS G 84 ASN ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1238 GLN ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.096311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.061798 restraints weight = 104989.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063048 restraints weight = 59301.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063486 restraints weight = 39819.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063513 restraints weight = 40069.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063526 restraints weight = 35421.094| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26777 Z= 0.172 Angle : 0.677 18.914 36449 Z= 0.339 Chirality : 0.045 0.273 4176 Planarity : 0.005 0.105 4544 Dihedral : 13.788 175.662 4375 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.66 % Allowed : 16.05 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3174 helix: 1.26 (0.16), residues: 1125 sheet: -0.26 (0.25), residues: 408 loop : -0.57 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 202 TYR 0.045 0.001 TYR J 679 PHE 0.020 0.001 PHE I 629 TRP 0.013 0.001 TRP I 997 HIS 0.007 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (26769) covalent geometry : angle 0.65027 / 0.34 (36437) hydrogen bonds : bond 0.04453 / 4.87 ( 1101) hydrogen bonds : angle 5.10121 / 5.42 ( 3035) metal coordination : bond 0.00731 / 0.79 ( 8) metal coordination : angle 10.32702 / 17.28 ( 12) *********************** 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 428 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 302 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7604 (ptpp) cc_final: 0.7258 (tmmt) REVERT: G 177 TYR cc_start: 0.7944 (m-80) cc_final: 0.7443 (m-80) REVERT: H 9 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8531 (tp) REVERT: H 35 PHE cc_start: 0.8886 (m-80) cc_final: 0.7744 (m-80) REVERT: H 51 MET cc_start: 0.8398 (mmm) cc_final: 0.8043 (mmm) REVERT: H 188 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7683 (mt-10) REVERT: H 200 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8463 (pptt) REVERT: I 100 LEU cc_start: 0.9217 (mt) cc_final: 0.8853 (tp) REVERT: I 325 LEU cc_start: 0.9658 (mm) cc_final: 0.9406 (pp) REVERT: I 389 PHE cc_start: 0.9520 (m-10) cc_final: 0.9307 (m-80) REVERT: I 538 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7511 (pp) REVERT: I 653 MET cc_start: 0.8271 (tmm) cc_final: 0.7823 (tmm) REVERT: I 775 GLU cc_start: 0.8408 (tt0) cc_final: 0.8156 (tt0) REVERT: I 829 THR cc_start: 0.9285 (m) cc_final: 0.8970 (p) REVERT: I 876 GLU cc_start: 0.8542 (tp30) cc_final: 0.8191 (tp30) REVERT: I 951 MET cc_start: 0.9252 (tmm) cc_final: 0.9009 (tmm) REVERT: I 1092 THR cc_start: 0.8988 (m) cc_final: 0.8509 (p) REVERT: I 1131 MET cc_start: 0.8963 (mtp) cc_final: 0.8648 (mtp) REVERT: I 1180 MET cc_start: 0.9068 (ttm) cc_final: 0.8739 (ttt) REVERT: I 1251 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: I 1289 GLU cc_start: 0.8087 (tt0) cc_final: 0.7259 (tm-30) REVERT: I 1290 MET cc_start: 0.9152 (tpp) cc_final: 0.8897 (tpp) REVERT: I 1294 LYS cc_start: 0.8716 (pttt) cc_final: 0.7083 (pttt) REVERT: I 1304 MET cc_start: 0.9209 (ttp) cc_final: 0.8747 (ptm) REVERT: J 128 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9040 (tp) REVERT: J 130 MET cc_start: 0.8894 (mmm) cc_final: 0.8253 (mmm) REVERT: J 160 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8954 (mm) REVERT: J 224 LEU cc_start: 0.9783 (mt) cc_final: 0.9524 (pp) REVERT: J 330 MET cc_start: 0.7417 (ptp) cc_final: 0.6482 (ptp) REVERT: J 340 GLN cc_start: 0.8681 (tp40) cc_final: 0.7957 (mm110) REVERT: J 484 MET cc_start: 0.8482 (mtm) cc_final: 0.8216 (mtm) REVERT: J 531 LYS cc_start: 0.8793 (mppt) cc_final: 0.8313 (mmmm) REVERT: J 649 LYS cc_start: 0.9720 (OUTLIER) cc_final: 0.8906 (tptt) REVERT: J 679 TYR cc_start: 0.9423 (p90) cc_final: 0.9146 (p90) REVERT: J 686 TRP cc_start: 0.9152 (m100) cc_final: 0.8573 (m100) REVERT: J 697 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8265 (tmm) REVERT: J 724 MET cc_start: 0.9017 (mtm) cc_final: 0.8744 (mtm) REVERT: J 747 MET cc_start: 0.7663 (mpt) cc_final: 0.7365 (mmm) REVERT: J 789 LYS cc_start: 0.7086 (mmtt) cc_final: 0.6590 (mttt) REVERT: J 822 MET cc_start: 0.8647 (mmm) cc_final: 0.8406 (ttt) REVERT: J 1040 MET cc_start: 0.6565 (mtt) cc_final: 0.6095 (mpp) REVERT: J 1189 MET cc_start: 0.9373 (tpp) cc_final: 0.8920 (tpp) REVERT: J 1190 ILE cc_start: 0.9513 (pt) cc_final: 0.9038 (mp) REVERT: K 8 ASP cc_start: 0.9284 (t0) cc_final: 0.8642 (t0) REVERT: K 12 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8793 (mmmt) REVERT: K 43 ASN cc_start: 0.8612 (t0) cc_final: 0.8388 (t0) REVERT: K 49 ILE cc_start: 0.9749 (pt) cc_final: 0.9380 (pt) REVERT: K 52 ARG cc_start: 0.9585 (mtp180) cc_final: 0.9043 (ptm160) outliers start: 126 outliers final: 96 residues processed: 395 average time/residue: 0.1440 time to fit residues: 91.7866 Evaluate side-chains 382 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 278 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 995 ASP Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1251 TYR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 549 LYS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 608 CYS Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 690 ASN Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1279 GLN Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 117 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN I 165 HIS ** I 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 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 = 0.3901 r_free = 0.3901 target = 0.096185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060514 restraints weight = 104017.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063347 restraints weight = 58612.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063206 restraints weight = 40751.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.063787 restraints weight = 33993.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063981 restraints weight = 31900.781| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26777 Z= 0.161 Angle : 0.654 16.853 36449 Z= 0.329 Chirality : 0.044 0.344 4176 Planarity : 0.004 0.071 4544 Dihedral : 13.803 175.276 4375 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.81 % Allowed : 15.98 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3174 helix: 1.21 (0.16), residues: 1127 sheet: -0.28 (0.25), residues: 407 loop : -0.59 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 67 TYR 0.036 0.001 TYR J 679 PHE 0.013 0.001 PHE I 629 TRP 0.047 0.002 TRP I 997 HIS 0.004 0.001 HIS J1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (26769) covalent geometry : angle 0.63159 / 0.33 (36437) hydrogen bonds : bond 0.04337 / 4.75 ( 1101) hydrogen bonds : angle 5.03691 / 5.42 ( 3035) metal coordination : bond 0.00658 / 0.72 ( 8) metal coordination : angle 9.47285 / 15.76 ( 12) *********************** 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 427 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 297 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7660 (ptpp) cc_final: 0.7340 (ptpp) REVERT: G 177 TYR cc_start: 0.7874 (m-80) cc_final: 0.7427 (m-80) REVERT: H 9 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8606 (tp) REVERT: H 35 PHE cc_start: 0.8845 (m-80) cc_final: 0.7731 (m-80) REVERT: H 51 MET cc_start: 0.8390 (mmm) cc_final: 0.8041 (mmm) REVERT: H 200 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8573 (pptt) REVERT: H 215 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: I 325 LEU cc_start: 0.9653 (mm) cc_final: 0.9404 (pp) REVERT: I 389 PHE cc_start: 0.9510 (m-10) cc_final: 0.9308 (m-80) REVERT: I 538 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7404 (pp) REVERT: I 653 MET cc_start: 0.8273 (tmm) cc_final: 0.7830 (tmm) REVERT: I 829 THR cc_start: 0.9278 (m) cc_final: 0.9001 (p) REVERT: I 876 GLU cc_start: 0.8369 (tp30) cc_final: 0.8164 (tp30) REVERT: I 1092 THR cc_start: 0.8993 (m) cc_final: 0.8522 (p) REVERT: I 1131 MET cc_start: 0.8783 (mtp) cc_final: 0.8506 (mtp) REVERT: I 1180 MET cc_start: 0.9050 (ttm) cc_final: 0.8734 (ttt) REVERT: I 1251 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6738 (m-80) REVERT: I 1289 GLU cc_start: 0.8002 (tt0) cc_final: 0.7204 (tm-30) REVERT: I 1290 MET cc_start: 0.9159 (tpp) cc_final: 0.8909 (tpp) REVERT: I 1294 LYS cc_start: 0.8711 (pttt) cc_final: 0.7068 (pttt) REVERT: I 1304 MET cc_start: 0.9151 (ttp) cc_final: 0.8665 (ptm) REVERT: J 128 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.8918 (tp) REVERT: J 130 MET cc_start: 0.8920 (mmm) cc_final: 0.8302 (mmm) REVERT: J 160 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8930 (mm) REVERT: J 224 LEU cc_start: 0.9773 (mt) cc_final: 0.9535 (pp) REVERT: J 340 GLN cc_start: 0.8682 (tp40) cc_final: 0.7985 (mm110) REVERT: J 484 MET cc_start: 0.8427 (mtm) cc_final: 0.8174 (mtm) REVERT: J 531 LYS cc_start: 0.8715 (mppt) cc_final: 0.8263 (mmmm) REVERT: J 549 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8690 (ttmm) REVERT: J 649 LYS cc_start: 0.9678 (OUTLIER) cc_final: 0.8894 (tptt) REVERT: J 679 TYR cc_start: 0.9388 (p90) cc_final: 0.9036 (p90) REVERT: J 686 TRP cc_start: 0.9067 (m100) cc_final: 0.8549 (m100) REVERT: J 697 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8150 (tmm) REVERT: J 747 MET cc_start: 0.7572 (mpt) cc_final: 0.7295 (mmm) REVERT: J 789 LYS cc_start: 0.7111 (mmtt) cc_final: 0.6799 (mttt) REVERT: J 822 MET cc_start: 0.8625 (mmm) cc_final: 0.8189 (ttt) REVERT: J 932 MET cc_start: 0.7020 (mmm) cc_final: 0.5960 (mtm) REVERT: J 935 PHE cc_start: 0.8404 (p90) cc_final: 0.8089 (p90) REVERT: J 1040 MET cc_start: 0.6629 (mtt) cc_final: 0.6320 (mtt) REVERT: J 1189 MET cc_start: 0.9352 (tpp) cc_final: 0.8967 (tpp) REVERT: J 1190 ILE cc_start: 0.9479 (pt) cc_final: 0.8974 (mp) REVERT: K 8 ASP cc_start: 0.9302 (t0) cc_final: 0.9043 (t0) REVERT: K 43 ASN cc_start: 0.8663 (t0) cc_final: 0.8418 (t0) REVERT: K 52 ARG cc_start: 0.9549 (mtp180) cc_final: 0.9198 (mtp180) REVERT: K 64 LEU cc_start: 0.9580 (mt) cc_final: 0.9242 (tt) outliers start: 130 outliers final: 99 residues processed: 398 average time/residue: 0.1520 time to fit residues: 96.6478 Evaluate side-chains 386 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 277 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 995 ASP Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1251 TYR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1275 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 549 LYS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 608 CYS Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 690 ASN Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 241 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 249 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 169 optimal weight: 0.0060 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS ** I 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.096769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063243 restraints weight = 104821.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063029 restraints weight = 65227.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064122 restraints weight = 46531.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.064145 restraints weight = 40984.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.064199 restraints weight = 37040.166| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26777 Z= 0.130 Angle : 0.660 16.125 36449 Z= 0.328 Chirality : 0.044 0.310 4176 Planarity : 0.004 0.087 4544 Dihedral : 13.764 175.291 4372 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.44 % Allowed : 17.38 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 3174 helix: 1.22 (0.16), residues: 1121 sheet: -0.39 (0.25), residues: 432 loop : -0.56 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 202 TYR 0.032 0.001 TYR J 679 PHE 0.013 0.001 PHE I 629 TRP 0.019 0.001 TRP I 997 HIS 0.008 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (26769) covalent geometry : angle 0.64066 / 0.33 (36437) hydrogen bonds : bond 0.04194 / 4.56 ( 1101) hydrogen bonds : angle 4.91863 / 5.27 ( 3035) metal coordination : bond 0.00561 / 0.61 ( 8) metal coordination : angle 8.79845 / 14.67 ( 12) *********************** 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 419 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 299 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7587 (ptpp) cc_final: 0.7380 (ptpp) REVERT: G 102 LEU cc_start: 0.8784 (tp) cc_final: 0.8131 (pp) REVERT: G 177 TYR cc_start: 0.7815 (m-80) cc_final: 0.7378 (m-80) REVERT: H 9 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8568 (tp) REVERT: H 35 PHE cc_start: 0.8826 (m-80) cc_final: 0.7696 (m-80) REVERT: H 51 MET cc_start: 0.8331 (mmm) cc_final: 0.7843 (mmm) REVERT: H 200 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8565 (pptt) REVERT: H 205 MET cc_start: 0.8739 (tpp) cc_final: 0.8509 (tpt) REVERT: H 215 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8384 (tp30) REVERT: H 226 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9098 (mm-30) REVERT: I 325 LEU cc_start: 0.9641 (mm) cc_final: 0.9389 (pp) REVERT: I 503 LYS cc_start: 0.9299 (pttm) cc_final: 0.9049 (ptpp) REVERT: I 538 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7464 (pp) REVERT: I 653 MET cc_start: 0.8291 (tmm) cc_final: 0.7847 (tmm) REVERT: I 829 THR cc_start: 0.9262 (m) cc_final: 0.8999 (p) REVERT: I 876 GLU cc_start: 0.8357 (tp30) cc_final: 0.8150 (tp30) REVERT: I 952 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8708 (pm20) REVERT: I 1092 THR cc_start: 0.8994 (m) cc_final: 0.8540 (p) REVERT: I 1131 MET cc_start: 0.8870 (mtp) cc_final: 0.8552 (mtp) REVERT: I 1251 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: I 1289 GLU cc_start: 0.7933 (tt0) cc_final: 0.7514 (tm-30) REVERT: J 102 MET cc_start: 0.8741 (tpp) cc_final: 0.8329 (tpp) REVERT: J 128 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.8959 (tp) REVERT: J 130 MET cc_start: 0.8973 (mmm) cc_final: 0.8351 (mmm) REVERT: J 160 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8972 (mm) REVERT: J 224 LEU cc_start: 0.9777 (mt) cc_final: 0.9539 (pp) REVERT: J 340 GLN cc_start: 0.8624 (tp40) cc_final: 0.7929 (mm110) REVERT: J 484 MET cc_start: 0.8374 (mtm) cc_final: 0.8128 (mtm) REVERT: J 525 MET cc_start: 0.7600 (ptp) cc_final: 0.7178 (ptp) REVERT: J 531 LYS cc_start: 0.8644 (mppt) cc_final: 0.8437 (mmmt) REVERT: J 549 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8679 (ttmm) REVERT: J 649 LYS cc_start: 0.9697 (OUTLIER) cc_final: 0.8927 (tptt) REVERT: J 679 TYR cc_start: 0.9402 (p90) cc_final: 0.9014 (p90) REVERT: J 686 TRP cc_start: 0.9066 (m100) cc_final: 0.8497 (m100) REVERT: J 697 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8202 (tmm) REVERT: J 747 MET cc_start: 0.7585 (mpt) cc_final: 0.7290 (mmm) REVERT: J 789 LYS cc_start: 0.7015 (mmtt) cc_final: 0.6647 (mttt) REVERT: J 1040 MET cc_start: 0.6633 (mtt) cc_final: 0.4996 (mpp) REVERT: J 1189 MET cc_start: 0.9375 (tpp) cc_final: 0.9019 (tpp) REVERT: J 1190 ILE cc_start: 0.9466 (pt) cc_final: 0.8958 (mp) REVERT: K 8 ASP cc_start: 0.9326 (t0) cc_final: 0.9073 (t0) REVERT: K 16 ARG cc_start: 0.9280 (mpp80) cc_final: 0.8816 (mpp80) REVERT: K 43 ASN cc_start: 0.8804 (t0) cc_final: 0.8557 (t0) REVERT: K 52 ARG cc_start: 0.9547 (mtp180) cc_final: 0.9180 (mtp180) REVERT: K 64 LEU cc_start: 0.9555 (mt) cc_final: 0.9236 (tp) REVERT: K 67 ARG cc_start: 0.9253 (ttp80) cc_final: 0.9004 (ttp80) outliers start: 120 outliers final: 96 residues processed: 392 average time/residue: 0.1555 time to fit residues: 98.1366 Evaluate side-chains 387 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 280 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 952 GLN Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 995 ASP Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1251 TYR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1275 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 549 LYS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 608 CYS Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 690 ASN Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 302 optimal weight: 0.9990 chunk 277 optimal weight: 50.0000 chunk 186 optimal weight: 20.0000 chunk 208 optimal weight: 40.0000 chunk 49 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 310 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN I 165 HIS ** I 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1279 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 = 0.3881 r_free = 0.3881 target = 0.095087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061451 restraints weight = 105296.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.061518 restraints weight = 66261.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062188 restraints weight = 45447.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062329 restraints weight = 42513.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.062428 restraints weight = 37792.896| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26777 Z= 0.229 Angle : 0.699 16.774 36449 Z= 0.355 Chirality : 0.045 0.306 4176 Planarity : 0.004 0.060 4544 Dihedral : 13.861 174.953 4372 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.36 % Allowed : 17.20 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3174 helix: 1.07 (0.15), residues: 1125 sheet: -0.38 (0.25), residues: 416 loop : -0.67 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 182 TYR 0.028 0.002 TYR J 679 PHE 0.016 0.001 PHE I 224 TRP 0.016 0.002 TRP I 997 HIS 0.007 0.001 HIS J1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (26769) covalent geometry : angle 0.68163 / 0.35 (36437) hydrogen bonds : bond 0.04517 / 4.85 ( 1101) hydrogen bonds : angle 5.17401 / 5.56 ( 3035) metal coordination : bond 0.00604 / 0.62 ( 8) metal coordination : angle 8.59689 / 14.17 ( 12) *********************** 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 425 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 280 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7514 (ptpp) cc_final: 0.7281 (ptpp) REVERT: G 86 LYS cc_start: 0.9422 (tptt) cc_final: 0.9221 (mmtt) REVERT: G 142 MET cc_start: 0.8681 (mmp) cc_final: 0.8470 (tpp) REVERT: G 177 TYR cc_start: 0.7803 (m-80) cc_final: 0.7398 (m-80) REVERT: H 9 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8571 (tp) REVERT: H 35 PHE cc_start: 0.8878 (m-80) cc_final: 0.7758 (m-80) REVERT: H 47 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8395 (mm) REVERT: H 51 MET cc_start: 0.8484 (mmm) cc_final: 0.7978 (mmm) REVERT: H 200 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8563 (pptt) REVERT: H 205 MET cc_start: 0.8742 (tpp) cc_final: 0.8483 (tpt) REVERT: H 215 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8403 (tp30) REVERT: H 226 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9081 (mm-30) REVERT: I 325 LEU cc_start: 0.9647 (mm) cc_final: 0.9402 (pp) REVERT: I 369 MET cc_start: 0.9099 (mmm) cc_final: 0.8871 (mmp) REVERT: I 503 LYS cc_start: 0.9322 (pttm) cc_final: 0.9047 (ptpp) REVERT: I 538 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7423 (pp) REVERT: I 653 MET cc_start: 0.8291 (tmm) cc_final: 0.7852 (tmm) REVERT: I 829 THR cc_start: 0.9290 (m) cc_final: 0.9017 (p) REVERT: I 1025 PHE cc_start: 0.9184 (m-80) cc_final: 0.8903 (m-80) REVERT: I 1092 THR cc_start: 0.8992 (m) cc_final: 0.8520 (p) REVERT: I 1131 MET cc_start: 0.8919 (mtp) cc_final: 0.8598 (mtp) REVERT: I 1251 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: I 1289 GLU cc_start: 0.8078 (tt0) cc_final: 0.7386 (tm-30) REVERT: I 1290 MET cc_start: 0.9246 (tpp) cc_final: 0.8801 (ttm) REVERT: I 1294 LYS cc_start: 0.8747 (pttt) cc_final: 0.7147 (pttt) REVERT: I 1333 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8485 (tp) REVERT: J 102 MET cc_start: 0.8797 (tpp) cc_final: 0.8497 (tpp) REVERT: J 128 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.8982 (tp) REVERT: J 130 MET cc_start: 0.8996 (mmm) cc_final: 0.8352 (mmm) REVERT: J 160 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9009 (mm) REVERT: J 224 LEU cc_start: 0.9794 (mt) cc_final: 0.9563 (pp) REVERT: J 340 GLN cc_start: 0.8716 (tp40) cc_final: 0.8036 (mm110) REVERT: J 484 MET cc_start: 0.8480 (mtm) cc_final: 0.8240 (mtm) REVERT: J 679 TYR cc_start: 0.9416 (p90) cc_final: 0.9000 (p90) REVERT: J 686 TRP cc_start: 0.9077 (m100) cc_final: 0.8487 (m100) REVERT: J 697 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8259 (tmm) REVERT: J 747 MET cc_start: 0.7576 (mpt) cc_final: 0.7247 (mmm) REVERT: J 789 LYS cc_start: 0.7198 (mmtt) cc_final: 0.6883 (mttt) REVERT: J 932 MET cc_start: 0.7131 (mmm) cc_final: 0.6255 (mtm) REVERT: J 935 PHE cc_start: 0.8568 (p90) cc_final: 0.8359 (p90) REVERT: J 1040 MET cc_start: 0.6795 (mtt) cc_final: 0.5031 (mpp) REVERT: J 1189 MET cc_start: 0.9406 (tpp) cc_final: 0.9044 (tpp) REVERT: J 1190 ILE cc_start: 0.9488 (pt) cc_final: 0.8976 (mp) REVERT: K 8 ASP cc_start: 0.9346 (t0) cc_final: 0.9082 (t0) REVERT: K 16 ARG cc_start: 0.9294 (mpp80) cc_final: 0.8806 (mpp80) REVERT: K 43 ASN cc_start: 0.8846 (t0) cc_final: 0.8611 (t0) REVERT: K 52 ARG cc_start: 0.9566 (mtp180) cc_final: 0.9097 (ptm160) REVERT: K 64 LEU cc_start: 0.9563 (mt) cc_final: 0.9249 (tp) REVERT: K 67 ARG cc_start: 0.9275 (ttp80) cc_final: 0.9062 (ttp80) outliers start: 145 outliers final: 115 residues processed: 394 average time/residue: 0.1550 time to fit residues: 98.0850 Evaluate side-chains 401 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 276 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 463 GLN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1251 TYR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1275 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain I residue 1333 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 325 LYS Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 549 LYS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 608 CYS Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 690 ASN Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 51 optimal weight: 0.1980 chunk 234 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 123 optimal weight: 0.0670 chunk 279 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 132 optimal weight: 30.0000 chunk 165 optimal weight: 3.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.096907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.063025 restraints weight = 103809.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.064616 restraints weight = 59222.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.064579 restraints weight = 39887.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.064748 restraints weight = 39049.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065077 restraints weight = 35528.812| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26777 Z= 0.121 Angle : 0.685 15.483 36449 Z= 0.341 Chirality : 0.045 0.335 4176 Planarity : 0.004 0.051 4544 Dihedral : 13.782 175.218 4372 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.88 % Allowed : 18.86 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3174 helix: 1.15 (0.16), residues: 1115 sheet: -0.47 (0.24), residues: 449 loop : -0.54 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 195 TYR 0.028 0.001 TYR J 679 PHE 0.017 0.001 PHE I 224 TRP 0.019 0.002 TRP I 997 HIS 0.007 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (26769) covalent geometry : angle 0.66927 / 0.34 (36437) hydrogen bonds : bond 0.04082 / 4.43 ( 1101) hydrogen bonds : angle 4.93005 / 5.30 ( 3035) metal coordination : bond 0.00504 / 0.56 ( 8) metal coordination : angle 7.96772 / 13.21 ( 12) *********************** 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 402 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 297 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7556 (ptpp) cc_final: 0.7326 (ptpp) REVERT: G 142 MET cc_start: 0.9017 (mmp) cc_final: 0.8556 (tpp) REVERT: G 177 TYR cc_start: 0.7724 (m-80) cc_final: 0.7297 (m-80) REVERT: H 9 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8589 (tp) REVERT: H 35 PHE cc_start: 0.8813 (m-80) cc_final: 0.8032 (m-80) REVERT: H 47 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8426 (mm) REVERT: H 51 MET cc_start: 0.8360 (mmm) cc_final: 0.7860 (mmm) REVERT: H 200 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8520 (pptt) REVERT: H 226 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9062 (mm-30) REVERT: I 315 MET cc_start: 0.8357 (mpp) cc_final: 0.7913 (pmm) REVERT: I 325 LEU cc_start: 0.9646 (mm) cc_final: 0.9401 (pp) REVERT: I 369 MET cc_start: 0.9095 (mmm) cc_final: 0.8796 (mmp) REVERT: I 503 LYS cc_start: 0.9261 (pttm) cc_final: 0.8966 (ptpt) REVERT: I 538 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7428 (pp) REVERT: I 653 MET cc_start: 0.8301 (tmm) cc_final: 0.7903 (tmm) REVERT: I 829 THR cc_start: 0.9274 (m) cc_final: 0.8992 (p) REVERT: I 1092 THR cc_start: 0.8992 (m) cc_final: 0.8542 (p) REVERT: I 1131 MET cc_start: 0.8826 (mtp) cc_final: 0.8505 (mtp) REVERT: I 1251 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: I 1289 GLU cc_start: 0.7921 (tt0) cc_final: 0.7517 (tm-30) REVERT: I 1290 MET cc_start: 0.9236 (tpp) cc_final: 0.8948 (ttm) REVERT: J 102 MET cc_start: 0.8782 (tpp) cc_final: 0.8581 (tpp) REVERT: J 128 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9177 (tp) REVERT: J 130 MET cc_start: 0.8984 (mmm) cc_final: 0.8636 (mmm) REVERT: J 224 LEU cc_start: 0.9794 (mt) cc_final: 0.9559 (pp) REVERT: J 340 GLN cc_start: 0.8609 (tp40) cc_final: 0.7928 (mm110) REVERT: J 525 MET cc_start: 0.7597 (ptp) cc_final: 0.7380 (ptp) REVERT: J 531 LYS cc_start: 0.8632 (mppt) cc_final: 0.8338 (mmmm) REVERT: J 549 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8683 (ttmm) REVERT: J 649 LYS cc_start: 0.9696 (OUTLIER) cc_final: 0.8912 (tptt) REVERT: J 679 TYR cc_start: 0.9420 (p90) cc_final: 0.8998 (p90) REVERT: J 686 TRP cc_start: 0.9035 (m100) cc_final: 0.8469 (m100) REVERT: J 697 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8193 (tmm) REVERT: J 747 MET cc_start: 0.7586 (mpt) cc_final: 0.7294 (mmm) REVERT: J 789 LYS cc_start: 0.7022 (mmtt) cc_final: 0.6608 (mttt) REVERT: J 932 MET cc_start: 0.7124 (mmm) cc_final: 0.6344 (mtm) REVERT: J 1040 MET cc_start: 0.6839 (mtt) cc_final: 0.5058 (mpp) REVERT: J 1189 MET cc_start: 0.9425 (tpp) cc_final: 0.9097 (tpp) REVERT: J 1190 ILE cc_start: 0.9470 (pt) cc_final: 0.8973 (mp) REVERT: K 8 ASP cc_start: 0.9368 (t0) cc_final: 0.9105 (t0) REVERT: K 43 ASN cc_start: 0.8904 (t0) cc_final: 0.8665 (t0) REVERT: K 52 ARG cc_start: 0.9556 (mtp180) cc_final: 0.9172 (mtp180) REVERT: K 64 LEU cc_start: 0.9560 (mt) cc_final: 0.9219 (tp) outliers start: 105 outliers final: 90 residues processed: 379 average time/residue: 0.1559 time to fit residues: 95.3060 Evaluate side-chains 375 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 276 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1251 TYR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1275 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 325 LYS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 549 LYS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 690 ASN Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 316 optimal weight: 0.0170 chunk 251 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 312 optimal weight: 0.0060 chunk 125 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 4 optimal weight: 50.0000 chunk 134 optimal weight: 9.9990 chunk 301 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 overall best weight: 2.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.096311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062983 restraints weight = 106211.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063277 restraints weight = 64771.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.063314 restraints weight = 45610.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.063609 restraints weight = 45393.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063808 restraints weight = 39095.764| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26777 Z= 0.150 Angle : 0.698 20.922 36449 Z= 0.351 Chirality : 0.044 0.312 4176 Planarity : 0.004 0.051 4544 Dihedral : 13.778 175.349 4372 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.11 % Allowed : 19.12 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3174 helix: 1.07 (0.16), residues: 1115 sheet: -0.47 (0.24), residues: 437 loop : -0.58 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 67 TYR 0.027 0.001 TYR J 679 PHE 0.018 0.001 PHE I 224 TRP 0.015 0.001 TRP I 997 HIS 0.004 0.001 HIS J1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (26769) covalent geometry : angle 0.68370 / 0.35 (36437) hydrogen bonds : bond 0.04158 / 4.47 ( 1101) hydrogen bonds : angle 5.03366 / 5.40 ( 3035) metal coordination : bond 0.00480 / 0.52 ( 8) metal coordination : angle 7.74670 / 12.79 ( 12) *********************** 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 397 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 286 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7531 (ptpp) cc_final: 0.7281 (ptpp) REVERT: G 142 MET cc_start: 0.9051 (mmp) cc_final: 0.8591 (tpp) REVERT: G 177 TYR cc_start: 0.7761 (m-80) cc_final: 0.7366 (m-80) REVERT: H 9 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8592 (tp) REVERT: H 35 PHE cc_start: 0.8826 (m-80) cc_final: 0.8049 (m-80) REVERT: H 47 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8403 (mm) REVERT: H 51 MET cc_start: 0.8407 (mmm) cc_final: 0.7914 (mmm) REVERT: H 200 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8519 (pptt) REVERT: H 215 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8404 (tp30) REVERT: H 226 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9094 (mm-30) REVERT: I 315 MET cc_start: 0.8328 (mpp) cc_final: 0.7944 (pmm) REVERT: I 325 LEU cc_start: 0.9636 (mm) cc_final: 0.9392 (pp) REVERT: I 369 MET cc_start: 0.9094 (mmm) cc_final: 0.8815 (mmp) REVERT: I 503 LYS cc_start: 0.9238 (pttm) cc_final: 0.8934 (ptpt) REVERT: I 538 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7396 (pp) REVERT: I 653 MET cc_start: 0.8258 (tmm) cc_final: 0.7861 (tmm) REVERT: I 1092 THR cc_start: 0.8967 (m) cc_final: 0.8522 (p) REVERT: I 1131 MET cc_start: 0.8837 (mtp) cc_final: 0.8592 (mtp) REVERT: I 1243 MET cc_start: 0.8423 (tmm) cc_final: 0.8193 (tmm) REVERT: I 1251 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6810 (m-80) REVERT: I 1289 GLU cc_start: 0.7939 (tt0) cc_final: 0.7563 (tm-30) REVERT: I 1290 MET cc_start: 0.9235 (tpp) cc_final: 0.8975 (ttm) REVERT: J 128 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9182 (tp) REVERT: J 130 MET cc_start: 0.9007 (mmm) cc_final: 0.8661 (mmm) REVERT: J 224 LEU cc_start: 0.9795 (mt) cc_final: 0.9565 (pp) REVERT: J 340 GLN cc_start: 0.8643 (tp40) cc_final: 0.7968 (mm110) REVERT: J 531 LYS cc_start: 0.8640 (mppt) cc_final: 0.8280 (mmmm) REVERT: J 549 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8693 (ttmm) REVERT: J 649 LYS cc_start: 0.9705 (OUTLIER) cc_final: 0.8923 (tptt) REVERT: J 679 TYR cc_start: 0.9419 (p90) cc_final: 0.8991 (p90) REVERT: J 686 TRP cc_start: 0.9028 (m100) cc_final: 0.8473 (m100) REVERT: J 697 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8218 (tmm) REVERT: J 747 MET cc_start: 0.7555 (mpt) cc_final: 0.7251 (mmm) REVERT: J 789 LYS cc_start: 0.7103 (mmtt) cc_final: 0.6758 (mttt) REVERT: J 932 MET cc_start: 0.7225 (mmm) cc_final: 0.6467 (mtm) REVERT: J 935 PHE cc_start: 0.8545 (p90) cc_final: 0.8330 (p90) REVERT: J 1040 MET cc_start: 0.6873 (mtt) cc_final: 0.5063 (mpp) REVERT: J 1189 MET cc_start: 0.9422 (tpp) cc_final: 0.9085 (tpp) REVERT: J 1190 ILE cc_start: 0.9470 (pt) cc_final: 0.8966 (mp) REVERT: K 8 ASP cc_start: 0.9378 (t0) cc_final: 0.9112 (t0) REVERT: K 43 ASN cc_start: 0.8938 (t0) cc_final: 0.8716 (t0) REVERT: K 52 ARG cc_start: 0.9563 (mtp180) cc_final: 0.9109 (ptm160) outliers start: 111 outliers final: 93 residues processed: 375 average time/residue: 0.1527 time to fit residues: 92.4035 Evaluate side-chains 373 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 270 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1251 TYR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1275 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 325 LYS Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 549 LYS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 690 ASN Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 105 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.096914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063664 restraints weight = 105145.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.063656 restraints weight = 65316.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.064379 restraints weight = 47229.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064657 restraints weight = 41100.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064644 restraints weight = 36385.097| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 26777 Z= 0.132 Angle : 0.725 18.250 36449 Z= 0.366 Chirality : 0.045 0.313 4176 Planarity : 0.004 0.050 4544 Dihedral : 13.749 175.664 4372 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.92 % Allowed : 19.64 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3174 helix: 1.01 (0.16), residues: 1123 sheet: -0.35 (0.25), residues: 440 loop : -0.60 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 67 TYR 0.027 0.001 TYR J 679 PHE 0.037 0.001 PHE I 389 TRP 0.016 0.001 TRP I 997 HIS 0.004 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (26769) covalent geometry : angle 0.71317 / 0.36 (36437) hydrogen bonds : bond 0.04140 / 4.45 ( 1101) hydrogen bonds : angle 4.99199 / 5.35 ( 3035) metal coordination : bond 0.00449 / 0.51 ( 8) metal coordination : angle 7.37346 / 12.18 ( 12) ********************** 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 387 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 281 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.7507 (ptpp) cc_final: 0.7258 (ptpp) REVERT: G 142 MET cc_start: 0.9051 (mmp) cc_final: 0.8595 (tpp) REVERT: G 177 TYR cc_start: 0.7777 (m-80) cc_final: 0.7353 (m-80) REVERT: H 9 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8592 (tp) REVERT: H 35 PHE cc_start: 0.8830 (m-80) cc_final: 0.8046 (m-80) REVERT: H 47 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8394 (mm) REVERT: H 51 MET cc_start: 0.8399 (mmm) cc_final: 0.7904 (mmm) REVERT: H 200 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8485 (pptt) REVERT: H 215 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8429 (tp30) REVERT: H 226 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9097 (mm-30) REVERT: I 100 LEU cc_start: 0.8799 (mm) cc_final: 0.8171 (tp) REVERT: I 315 MET cc_start: 0.8331 (mpp) cc_final: 0.7959 (pmm) REVERT: I 325 LEU cc_start: 0.9650 (mm) cc_final: 0.9406 (pp) REVERT: I 369 MET cc_start: 0.9136 (mmm) cc_final: 0.8836 (mmp) REVERT: I 503 LYS cc_start: 0.9286 (pttm) cc_final: 0.8979 (ptpt) REVERT: I 538 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7453 (pp) REVERT: I 653 MET cc_start: 0.8290 (tmm) cc_final: 0.7896 (tmm) REVERT: I 660 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9172 (t) REVERT: I 1092 THR cc_start: 0.8981 (m) cc_final: 0.8525 (p) REVERT: I 1126 ASP cc_start: 0.8837 (t70) cc_final: 0.8446 (m-30) REVERT: I 1131 MET cc_start: 0.8846 (mtp) cc_final: 0.8609 (mtp) REVERT: I 1278 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8705 (tm) REVERT: I 1289 GLU cc_start: 0.7991 (tt0) cc_final: 0.7453 (tm-30) REVERT: I 1290 MET cc_start: 0.9225 (tpp) cc_final: 0.8877 (ttm) REVERT: J 102 MET cc_start: 0.7729 (tpp) cc_final: 0.7270 (tpp) REVERT: J 128 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9180 (tp) REVERT: J 130 MET cc_start: 0.8998 (mmm) cc_final: 0.8656 (mmm) REVERT: J 224 LEU cc_start: 0.9803 (mt) cc_final: 0.9574 (pp) REVERT: J 340 GLN cc_start: 0.8605 (tp40) cc_final: 0.7911 (mm110) REVERT: J 531 LYS cc_start: 0.8639 (mppt) cc_final: 0.8170 (mmmm) REVERT: J 549 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8681 (ttmm) REVERT: J 649 LYS cc_start: 0.9710 (OUTLIER) cc_final: 0.8916 (tptt) REVERT: J 679 TYR cc_start: 0.9440 (p90) cc_final: 0.9021 (p90) REVERT: J 686 TRP cc_start: 0.9037 (m100) cc_final: 0.8474 (m100) REVERT: J 697 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8253 (tmm) REVERT: J 747 MET cc_start: 0.7554 (mpt) cc_final: 0.7274 (mmm) REVERT: J 789 LYS cc_start: 0.7042 (mmtt) cc_final: 0.6615 (mttt) REVERT: J 932 MET cc_start: 0.7208 (mmm) cc_final: 0.6501 (mtm) REVERT: J 1040 MET cc_start: 0.7037 (mtt) cc_final: 0.5238 (mpp) REVERT: J 1189 MET cc_start: 0.9438 (tpp) cc_final: 0.9120 (tpp) REVERT: J 1190 ILE cc_start: 0.9494 (pt) cc_final: 0.9006 (mp) REVERT: J 1366 HIS cc_start: 0.9267 (OUTLIER) cc_final: 0.9057 (m-70) REVERT: K 8 ASP cc_start: 0.9382 (t0) cc_final: 0.9111 (t0) REVERT: K 43 ASN cc_start: 0.8950 (t0) cc_final: 0.8729 (t0) REVERT: K 52 ARG cc_start: 0.9566 (mtp180) cc_final: 0.9112 (ptm160) outliers start: 106 outliers final: 87 residues processed: 366 average time/residue: 0.1454 time to fit residues: 85.8270 Evaluate side-chains 368 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 269 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 185 TYR Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1275 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 325 LYS Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 549 LYS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 690 ASN Chi-restraints excluded: chain J residue 697 MET Chi-restraints excluded: chain J residue 727 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 1081 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 275 optimal weight: 0.0470 chunk 107 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 954 ASN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.096646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063444 restraints weight = 105678.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.063845 restraints weight = 64266.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064128 restraints weight = 43980.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064230 restraints weight = 46482.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064554 restraints weight = 39422.530| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26777 Z= 0.140 Angle : 0.737 17.916 36449 Z= 0.373 Chirality : 0.045 0.300 4176 Planarity : 0.004 0.051 4544 Dihedral : 13.746 179.348 4369 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.88 % Allowed : 19.71 % Favored : 76.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3174 helix: 0.97 (0.16), residues: 1119 sheet: -0.43 (0.24), residues: 448 loop : -0.59 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG K 25 TYR 0.026 0.001 TYR J 679 PHE 0.040 0.001 PHE I 389 TRP 0.014 0.002 TRP J 115 HIS 0.005 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (26769) covalent geometry : angle 0.72500 / 0.37 (36437) hydrogen bonds : bond 0.04222 / 4.50 ( 1101) hydrogen bonds : angle 5.00635 / 5.39 ( 3035) metal coordination : bond 0.00435 / 0.49 ( 8) metal coordination : angle 7.21223 / 11.86 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5086.16 seconds wall clock time: 88 minutes 22.61 seconds (5302.61 seconds total)