Starting phenix.real_space_refine on Sat Aug 8 22:58:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8toe_41448/08_2026/8toe_41448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8toe_41448/08_2026/8toe_41448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8toe_41448/08_2026/8toe_41448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8toe_41448/08_2026/8toe_41448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8toe_41448/08_2026/8toe_41448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8toe_41448/08_2026/8toe_41448.map" } resolution = 2.9 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= 0.003 sd= 0.068 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 74 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19227 2.51 5 N 5480 2.21 5 O 6082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 30996 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1773 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1685 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 10518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10518 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10381 Classifications: {'peptide': 1335} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Chain: "K" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "L" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3858 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 13, 'TRANS': 468} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "O" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 820 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "P" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "L" 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14425 SG CYS J 70 102.368 69.778 74.219 1.00 90.31 S ATOM 14439 SG CYS J 72 100.808 66.671 73.069 1.00 85.05 S ATOM 14547 SG CYS J 85 104.262 67.505 71.839 1.00 84.26 S ATOM 14571 SG CYS J 88 101.866 70.658 72.431 1.00 82.21 S ATOM 20259 SG CYS J 814 131.341 120.129 110.560 1.00 64.85 S ATOM 20824 SG CYS J 888 127.706 119.034 108.876 1.00 47.14 S ATOM 20875 SG CYS J 895 129.128 117.778 112.235 1.00 48.23 S ATOM 20896 SG CYS J 898 128.474 120.654 112.335 1.00 45.04 S Time building chain proxies: 5.64, per 1000 atoms: 0.18 Number of scatterers: 30996 At special positions: 0 Unit cell: (153.608, 196.652, 194.12, 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 130 16.00 P 74 15.00 Mg 1 11.99 O 6082 8.00 N 5480 7.00 C 19227 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: 2.59 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 47 sheets defined 44.0% alpha, 14.4% beta 32 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.766A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.739A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 233 removed outlier: 4.181A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.554A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 87 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 212 through 228 removed outlier: 3.758A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 4.137A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 81 through 88 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.910A 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 270 through 280 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.846A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 removed outlier: 3.771A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.982A pdb=" N GLU I 461 " --> pdb=" O GLY I 457 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN I 463 " --> pdb=" O MET I 459 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.463A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 539 through 543 removed outlier: 3.639A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.534A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.711A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.611A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 4.023A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 899 through 907 Processing helix chain 'I' and resid 942 through 978 removed outlier: 3.758A pdb=" N ALA I 969 " --> pdb=" O GLN I 965 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY I 970 " --> pdb=" O ILE I 966 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU I 971 " --> pdb=" O LEU I 967 " (cutoff:3.500A) Processing helix chain 'I' and resid 988 through 992 Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.681A pdb=" N TRP I 997 " --> pdb=" O ARG I 994 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.423A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.737A 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 removed outlier: 3.586A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1149 removed outlier: 3.750A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.727A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 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 1281 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.696A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.623A pdb=" N LYS I1306 " --> pdb=" O THR I1302 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.756A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 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: 3.557A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.582A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 170 removed outlier: 3.608A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.670A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 231 removed outlier: 3.867A pdb=" N GLY J 231 " --> pdb=" O PHE J 227 " (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 264 through 286 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.983A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) 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 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 580 Processing helix chain 'J' and resid 589 through 593 removed outlier: 3.601A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.706A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER J 602 " --> pdb=" O LYS J 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.562A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.673A 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 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.528A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.551A pdb=" N PHE J 773 " --> pdb=" O VAL J 769 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE J 774 " --> pdb=" O LEU J 770 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER J 775 " --> pdb=" O GLN J 771 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG J 780 " --> pdb=" O THR J 776 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.545A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) 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 925 removed outlier: 3.569A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1224 removed outlier: 3.723A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.618A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP J1239 " --> pdb=" O ASN J1235 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR J1241 " --> pdb=" O VAL J1237 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1259 removed outlier: 3.754A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN J1259 " --> pdb=" O VAL J1255 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1313 removed outlier: 3.528A pdb=" N SER J1313 " --> pdb=" O ILE J1309 " (cutoff:3.500A) Processing helix chain 'J' and resid 1314 through 1316 No H-bonds generated for 'chain 'J' and resid 1314 through 1316' Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.965A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1348 through 1354 removed outlier: 3.586A pdb=" N VAL J1353 " --> pdb=" O GLU J1349 " (cutoff:3.500A) Processing helix chain 'J' and resid 1362 through 1374 removed outlier: 3.504A pdb=" N ARG J1371 " --> pdb=" O GLN J1367 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.656A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 77 Processing helix chain 'L' and resid 10 through 15 Processing helix chain 'L' and resid 42 through 48 Processing helix chain 'L' and resid 96 through 107 removed outlier: 3.680A pdb=" N MET L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 136 removed outlier: 3.878A pdb=" N GLU L 116 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE L 119 " --> pdb=" O GLY L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 153 removed outlier: 4.297A pdb=" N THR L 142 " --> pdb=" O PRO L 138 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 162 removed outlier: 3.535A pdb=" N LEU L 161 " --> pdb=" O ARG L 157 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 162' Processing helix chain 'L' and resid 216 through 233 Processing helix chain 'L' and resid 244 through 259 removed outlier: 3.657A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE L 259 " --> pdb=" O VAL L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 293 Processing helix chain 'L' and resid 298 through 307 removed outlier: 3.729A pdb=" N PHE L 302 " --> pdb=" O PRO L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 318 Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 392 removed outlier: 3.704A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE L 388 " --> pdb=" O LEU L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 419 removed outlier: 3.510A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 446 removed outlier: 3.806A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR L 432 " --> pdb=" O SER L 428 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 491 through 501 removed outlier: 4.080A pdb=" N LYS L 499 " --> pdb=" O ARG L 495 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA L 501 " --> pdb=" O VAL L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.604A pdb=" N ASP L 521 " --> pdb=" O HIS L 518 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE L 522 " --> pdb=" O LEU L 519 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 518 through 523' Processing helix chain 'L' and resid 530 through 550 Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 585 through 600 Processing helix chain 'L' and resid 605 through 610 removed outlier: 3.598A pdb=" N SER L 609 " --> pdb=" O GLU L 605 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE L 610 " --> pdb=" O VAL L 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 605 through 610' Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 263 through 274 Processing helix chain 'M' and resid 277 through 283 Processing helix chain 'M' and resid 285 through 292 removed outlier: 3.587A pdb=" N THR M 292 " --> pdb=" O GLU M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 310 removed outlier: 3.606A pdb=" N ARG M 310 " --> pdb=" O VAL M 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 17 through 18 removed outlier: 5.549A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.604A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.611A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 20 removed outlier: 6.647A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 14 through 20 removed outlier: 6.647A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP H 197 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA H 190 " --> pdb=" O ASP H 197 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP H 199 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU H 188 " --> pdb=" O ASP H 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 61 removed outlier: 3.527A pdb=" N GLN H 147 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA H 138 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY H 106 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.771A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.885A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.004A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 284 through 286 removed outlier: 3.733A pdb=" N GLU I 240 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 616 through 617 removed outlier: 3.808A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.373A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.623A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.083A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.817A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.969A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.672A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 1338 through 1339 Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.739A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.728A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'J' and resid 703 through 705 Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.211A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.641A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.139A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.375A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1087 through 1088 removed outlier: 4.575A pdb=" N ILE J1080 " --> pdb=" O VAL J1088 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL J1035 " --> pdb=" O VAL J1113 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL J1113 " --> pdb=" O VAL J1035 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 3.665A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1188 through 1190 Processing sheet with id=AF2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.485A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) 1298 hydrogen bonds defined for protein. 3648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 9.51 Time building geometry restraints manager: 3.23 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: 10317 1.34 - 1.46: 6564 1.46 - 1.58: 14334 1.58 - 1.71: 154 1.71 - 1.83: 237 Bond restraints: 31606 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.828 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.826 -0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.823 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.735 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.729 -0.197 2.00e-02 2.50e+03 9.70e+01 ... (remaining 31601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 42938 3.94 - 7.87: 67 7.87 - 11.81: 3 11.81 - 15.74: 1 15.74 - 19.68: 1 Bond angle restraints: 43010 Sorted by residual: angle pdb=" O3' DG O 74 " pdb=" P DA O 75 " pdb=" OP2 DA O 75 " ideal model delta sigma weight residual 108.00 127.68 -19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" C ILE J 707 " pdb=" N ASN J 708 " pdb=" CA ASN J 708 " ideal model delta sigma weight residual 121.70 132.33 -10.63 1.80e+00 3.09e-01 3.49e+01 angle pdb=" O3' DG O 74 " pdb=" P DA O 75 " pdb=" O5' DA O 75 " ideal model delta sigma weight residual 104.00 94.62 9.38 1.90e+00 2.77e-01 2.44e+01 angle pdb=" O3' DG O 74 " pdb=" P DA O 75 " pdb=" OP1 DA O 75 " ideal model delta sigma weight residual 108.00 94.09 13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" N3 DT O 60 " pdb=" C4 DT O 60 " pdb=" O4 DT O 60 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 43005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 18970 35.33 - 70.66: 457 70.66 - 106.00: 14 106.00 - 141.33: 3 141.33 - 176.66: 2 Dihedral angle restraints: 19446 sinusoidal: 8642 harmonic: 10804 Sorted by residual: dihedral pdb=" CA LEU L 488 " pdb=" C LEU L 488 " pdb=" N MET L 489 " pdb=" CA MET L 489 " ideal model delta harmonic sigma weight residual 180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA MET L 487 " pdb=" C MET L 487 " pdb=" N LEU L 488 " pdb=" CA LEU L 488 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR I 742 " pdb=" C TYR I 742 " pdb=" N PRO I 743 " pdb=" CA PRO I 743 " ideal model delta harmonic sigma weight residual 180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 19443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4535 0.087 - 0.173: 393 0.173 - 0.260: 7 0.260 - 0.347: 6 0.347 - 0.434: 3 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.97 0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" C19 1N7 L 701 " pdb=" C18 1N7 L 701 " pdb=" C2 1N7 L 701 " pdb=" C3 1N7 L 701 " both_signs ideal model delta sigma weight residual False -2.53 -2.96 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.92 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 4941 not shown) Planarity restraints: 5337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I1223 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO I1224 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO I1224 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I1224 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 477 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO L 478 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 478 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 478 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 551 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO I 552 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO I 552 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 552 " 0.021 5.00e-02 4.00e+02 ... (remaining 5334 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 277 2.58 - 3.16: 25965 3.16 - 3.74: 45044 3.74 - 4.32: 63778 4.32 - 4.90: 108863 Nonbonded interactions: 243927 Sorted by model distance: nonbonded pdb=" OD1 ASP H 15 " pdb=" OG1 THR H 27 " model vdw 2.000 3.040 nonbonded pdb=" OG1 THR I 91 " pdb=" O ILE I 138 " model vdw 2.040 3.040 nonbonded pdb=" OG SER J1057 " pdb=" OE2 GLU J1110 " model vdw 2.084 3.040 nonbonded pdb=" OG1 THR L 234 " pdb=" OE1 GLU L 248 " model vdw 2.116 3.040 nonbonded pdb=" N SER L 602 " pdb=" OE2 GLU L 605 " model vdw 2.149 3.120 ... (remaining 243922 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 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 158 or resid 171 through 234)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 or (resid 193 through 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 234)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.610 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: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 35.010 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.006 0.296 31614 Z= 0.318 Angle : 0.684 56.527 43022 Z= 0.366 Chirality : 0.047 0.434 4944 Planarity : 0.003 0.054 5337 Dihedral : 13.704 176.661 12474 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.82 % Allowed : 5.40 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: 0.05 (0.14), residues: 3721 helix: 1.60 (0.14), residues: 1448 sheet: -0.36 (0.26), residues: 411 loop : -1.17 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 218 TYR 0.012 0.001 TYR G 177 PHE 0.013 0.001 PHE I 545 TRP 0.008 0.001 TRP I 807 HIS 0.003 0.001 HIS J 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.32 (31606) covalent geometry : angle 0.58752 / 0.36 (43010) hydrogen bonds : bond 0.17445 / 11.85 ( 1372) hydrogen bonds : angle 6.30696 / 4.34 ( 3810) metal coordination : bond 0.04073 / 2.31 ( 8) metal coordination : angle 21.01041 / 13.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 535 time to evaluate : 1.163 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: H 21 SER cc_start: 0.9078 (t) cc_final: 0.8762 (t) REVERT: H 79 LEU cc_start: 0.8031 (tt) cc_final: 0.7720 (tp) REVERT: H 152 TYR cc_start: 0.8575 (t80) cc_final: 0.8373 (t80) REVERT: I 36 GLN cc_start: 0.8316 (tt0) cc_final: 0.8099 (tt0) REVERT: I 414 ILE cc_start: 0.8077 (mm) cc_final: 0.7839 (tt) REVERT: I 516 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: I 706 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7964 (mtt-85) REVERT: I 768 MET cc_start: 0.8670 (ptm) cc_final: 0.8301 (ptp) REVERT: I 779 ARG cc_start: 0.8092 (ttt-90) cc_final: 0.7871 (ttm170) REVERT: I 814 ASP cc_start: 0.8247 (m-30) cc_final: 0.7990 (m-30) REVERT: I 912 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6426 (p0) REVERT: I 943 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7331 (mtmt) REVERT: I 1170 MET cc_start: 0.8566 (mmm) cc_final: 0.8345 (mmm) REVERT: I 1178 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7805 (mtmt) REVERT: J 60 ARG cc_start: 0.8142 (ptm-80) cc_final: 0.7841 (ptp-170) REVERT: J 130 MET cc_start: 0.8160 (mtp) cc_final: 0.7850 (mtm) REVERT: J 293 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7317 (ttp-110) REVERT: J 698 MET cc_start: 0.8124 (tpp) cc_final: 0.7877 (tpt) REVERT: J 781 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7753 (mtmm) REVERT: J 875 ASN cc_start: 0.7384 (m-40) cc_final: 0.7166 (m110) REVERT: J 1227 HIS cc_start: 0.8440 (m170) cc_final: 0.8228 (m170) REVERT: J 1244 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7832 (mp10) REVERT: J 1287 ILE cc_start: 0.7460 (pt) cc_final: 0.7169 (pp) REVERT: J 1311 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7692 (ttmt) REVERT: L 322 MET cc_start: 0.2260 (mtt) cc_final: 0.1654 (ptp) REVERT: L 388 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.6871 (mt) REVERT: L 489 MET cc_start: 0.8515 (mtm) cc_final: 0.8244 (mtm) outliers start: 58 outliers final: 17 residues processed: 582 average time/residue: 0.7060 time to fit residues: 480.6443 Evaluate side-chains 379 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 359 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 402 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0000 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.0970 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN H 18 GLN H 103 ASN ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN J 80 HIS J 229 GLN J1244 GLN K 62 GLN L 345 GLN L 396 ASN L 409 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.211136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122870 restraints weight = 33457.746| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.29 r_work: 0.3203 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 31614 Z= 0.154 Angle : 0.645 34.517 43022 Z= 0.328 Chirality : 0.044 0.296 4944 Planarity : 0.005 0.064 5337 Dihedral : 14.220 179.780 5149 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 3.11 % Allowed : 11.58 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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 (0.14), residues: 3721 helix: 1.60 (0.14), residues: 1482 sheet: -0.33 (0.26), residues: 408 loop : -1.13 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 101 TYR 0.021 0.001 TYR J 144 PHE 0.020 0.001 PHE L 419 TRP 0.006 0.001 TRP J 409 HIS 0.004 0.001 HIS J 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (31606) covalent geometry : angle 0.61347 / 0.33 (43010) hydrogen bonds : bond 0.05288 / 3.65 ( 1372) hydrogen bonds : angle 4.86183 / 3.33 ( 3810) metal coordination : bond 0.01226 / 0.65 ( 8) metal coordination : angle 11.90441 / 8.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 368 time to evaluate : 1.173 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: G 56 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8096 (t) REVERT: G 95 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8012 (ptpp) REVERT: H 79 LEU cc_start: 0.8095 (tt) cc_final: 0.7479 (mt) REVERT: I 28 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8665 (pp) REVERT: I 40 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: I 130 MET cc_start: 0.9310 (ttm) cc_final: 0.9068 (ttm) REVERT: I 185 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6584 (m-30) REVERT: I 473 ARG cc_start: 0.7332 (ttp80) cc_final: 0.6424 (ttp80) REVERT: I 510 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: I 706 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8132 (mtt-85) REVERT: I 745 GLU cc_start: 0.7911 (pt0) cc_final: 0.7662 (pt0) REVERT: I 768 MET cc_start: 0.8757 (ptm) cc_final: 0.8285 (ptp) REVERT: I 779 ARG cc_start: 0.8466 (ttt-90) cc_final: 0.8002 (ttm170) REVERT: I 912 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6560 (p0) REVERT: I 943 LYS cc_start: 0.7734 (mtpt) cc_final: 0.7465 (mtpm) REVERT: I 1082 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8028 (mp) REVERT: I 1140 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7713 (mmmm) REVERT: I 1150 ASP cc_start: 0.8386 (p0) cc_final: 0.8096 (p0) REVERT: I 1156 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8144 (ptt180) REVERT: J 60 ARG cc_start: 0.8506 (ptm-80) cc_final: 0.7683 (ptp-170) REVERT: J 130 MET cc_start: 0.8379 (mtp) cc_final: 0.8070 (mtm) REVERT: J 158 GLN cc_start: 0.7182 (tp40) cc_final: 0.6819 (tp40) REVERT: J 466 MET cc_start: 0.9274 (mtt) cc_final: 0.9003 (mtt) REVERT: J 652 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6941 (tt0) REVERT: J 663 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: J 781 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7594 (mtmm) REVERT: J 875 ASN cc_start: 0.7378 (m-40) cc_final: 0.7053 (m110) REVERT: J 1189 MET cc_start: 0.7766 (ptm) cc_final: 0.7154 (tmt) REVERT: J 1289 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6437 (m-40) REVERT: J 1311 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7775 (ttmt) REVERT: L 100 MET cc_start: 0.6948 (mtm) cc_final: 0.6738 (mtm) REVERT: L 322 MET cc_start: 0.3327 (mtt) cc_final: 0.2755 (ptp) REVERT: L 509 THR cc_start: 0.8048 (t) cc_final: 0.7113 (m) REVERT: L 538 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7627 (mp0) outliers start: 99 outliers final: 34 residues processed: 435 average time/residue: 0.6709 time to fit residues: 344.3341 Evaluate side-chains 389 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 344 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 719 LYS Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 394 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 56 optimal weight: 1.9990 chunk 368 optimal weight: 50.0000 chunk 188 optimal weight: 0.0870 chunk 346 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 252 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 18 GLN H 103 ASN H 227 GLN I 83 GLN I 618 GLN I 628 HIS I 811 ASN J 777 HIS L 362 ASN L 396 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.215201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.128192 restraints weight = 33748.149| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.59 r_work: 0.3165 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31614 Z= 0.151 Angle : 0.580 18.470 43022 Z= 0.301 Chirality : 0.043 0.287 4944 Planarity : 0.004 0.060 5337 Dihedral : 13.852 179.825 5135 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.89 % Rotamer: Outliers : 3.29 % Allowed : 13.56 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: 0.14 (0.14), residues: 3721 helix: 1.63 (0.14), residues: 1480 sheet: -0.32 (0.25), residues: 416 loop : -1.13 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J1371 TYR 0.022 0.001 TYR J 144 PHE 0.012 0.001 PHE L 427 TRP 0.006 0.001 TRP J 409 HIS 0.004 0.001 HIS J 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (31606) covalent geometry : angle 0.56697 / 0.30 (43010) hydrogen bonds : bond 0.04637 / 3.20 ( 1372) hydrogen bonds : angle 4.49300 / 3.08 ( 3810) metal coordination : bond 0.00911 / 0.51 ( 8) metal coordination : angle 7.30763 / 4.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 344 time to evaluate : 1.144 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: G 56 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8150 (t) REVERT: G 95 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8088 (ptpp) REVERT: G 187 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8654 (t) REVERT: H 79 LEU cc_start: 0.8111 (tt) cc_final: 0.7547 (mt) REVERT: I 28 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8669 (pp) REVERT: I 40 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: I 130 MET cc_start: 0.9314 (ttm) cc_final: 0.9111 (ttm) REVERT: I 510 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: I 538 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8164 (pp) REVERT: I 706 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8204 (mtt-85) REVERT: I 768 MET cc_start: 0.8841 (ptm) cc_final: 0.8382 (ptp) REVERT: I 779 ARG cc_start: 0.8514 (ttt-90) cc_final: 0.8066 (ttm170) REVERT: I 912 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6826 (p0) REVERT: I 940 GLU cc_start: 0.7516 (pp20) cc_final: 0.7301 (pp20) REVERT: I 943 LYS cc_start: 0.7727 (mtpt) cc_final: 0.7501 (mtpm) REVERT: I 1082 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8096 (mp) REVERT: I 1150 ASP cc_start: 0.8464 (p0) cc_final: 0.8184 (p0) REVERT: I 1156 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8241 (ptt180) REVERT: J 60 ARG cc_start: 0.8533 (ptm-80) cc_final: 0.7701 (ptp-170) REVERT: J 83 VAL cc_start: 0.8855 (p) cc_final: 0.8520 (m) REVERT: J 130 MET cc_start: 0.8327 (mtp) cc_final: 0.8061 (mtm) REVERT: J 599 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7283 (mmtm) REVERT: J 652 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7021 (tt0) REVERT: J 663 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: J 875 ASN cc_start: 0.7421 (m-40) cc_final: 0.7167 (m110) REVERT: J 1189 MET cc_start: 0.7715 (ptm) cc_final: 0.7065 (tmt) REVERT: J 1236 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: J 1289 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.6397 (m-40) REVERT: J 1311 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7783 (ttmt) REVERT: L 100 MET cc_start: 0.7064 (mtm) cc_final: 0.6838 (mtm) REVERT: L 110 LEU cc_start: 0.8670 (pp) cc_final: 0.8387 (mp) REVERT: L 322 MET cc_start: 0.3583 (mtt) cc_final: 0.3051 (ptp) REVERT: L 440 THR cc_start: 0.8211 (m) cc_final: 0.7766 (p) REVERT: L 509 THR cc_start: 0.8123 (t) cc_final: 0.7142 (m) REVERT: L 538 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7664 (mp0) REVERT: L 558 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7815 (p) REVERT: L 611 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8097 (pp) REVERT: M 262 LEU cc_start: 0.7725 (pt) cc_final: 0.6528 (pp) REVERT: M 270 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8803 (pt) outliers start: 105 outliers final: 48 residues processed: 417 average time/residue: 0.6630 time to fit residues: 327.6340 Evaluate side-chains 386 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 322 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 599 LYS Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 394 TYR Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 611 LEU Chi-restraints excluded: chain M residue 270 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 246 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 375 optimal weight: 30.0000 chunk 223 optimal weight: 1.9990 chunk 374 optimal weight: 50.0000 chunk 215 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 18 GLN H 103 ASN I 811 ASN J 157 GLN J 777 HIS J1249 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.208992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119524 restraints weight = 33558.454| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.97 r_work: 0.3216 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31614 Z= 0.154 Angle : 0.582 20.999 43022 Z= 0.299 Chirality : 0.043 0.295 4944 Planarity : 0.004 0.061 5337 Dihedral : 13.824 179.640 5133 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 3.58 % Allowed : 14.18 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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 (0.14), residues: 3721 helix: 1.61 (0.14), residues: 1494 sheet: -0.29 (0.25), residues: 416 loop : -1.18 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J1371 TYR 0.019 0.001 TYR G 177 PHE 0.012 0.001 PHE I 57 TRP 0.006 0.001 TRP J 409 HIS 0.005 0.001 HIS I 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (31606) covalent geometry : angle 0.56651 / 0.30 (43010) hydrogen bonds : bond 0.04422 / 3.04 ( 1372) hydrogen bonds : angle 4.34497 / 2.97 ( 3810) metal coordination : bond 0.01061 / 0.58 ( 8) metal coordination : angle 8.07534 / 5.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 331 time to evaluate : 1.117 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: G 33 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7825 (tpm170) REVERT: G 95 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8118 (ptpp) REVERT: G 181 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: G 187 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8660 (t) REVERT: H 79 LEU cc_start: 0.8092 (tt) cc_final: 0.7519 (mt) REVERT: I 28 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8659 (pp) REVERT: I 40 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7002 (mt-10) REVERT: I 510 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: I 768 MET cc_start: 0.8797 (ptm) cc_final: 0.8316 (ptp) REVERT: I 779 ARG cc_start: 0.8437 (ttt-90) cc_final: 0.7991 (ttm170) REVERT: I 912 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6747 (p0) REVERT: I 940 GLU cc_start: 0.7582 (pp20) cc_final: 0.7325 (pp20) REVERT: I 943 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7514 (mtpm) REVERT: I 1028 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7558 (tttt) REVERT: I 1082 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8088 (mp) REVERT: I 1140 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7682 (mtmt) REVERT: I 1150 ASP cc_start: 0.8414 (p0) cc_final: 0.8194 (p0) REVERT: I 1211 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8014 (ptm160) REVERT: J 60 ARG cc_start: 0.8477 (ptm-80) cc_final: 0.7682 (ptp-170) REVERT: J 83 VAL cc_start: 0.8849 (p) cc_final: 0.8506 (m) REVERT: J 130 MET cc_start: 0.8252 (mtp) cc_final: 0.7983 (mtm) REVERT: J 321 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8095 (mmmt) REVERT: J 599 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7250 (mmtm) REVERT: J 652 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6960 (tt0) REVERT: J 663 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: J 875 ASN cc_start: 0.7420 (m-40) cc_final: 0.7154 (m110) REVERT: J 1046 ILE cc_start: -0.0594 (OUTLIER) cc_final: -0.0829 (mp) REVERT: J 1189 MET cc_start: 0.7727 (ptm) cc_final: 0.7119 (tmt) REVERT: J 1236 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: J 1244 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7888 (mm-40) REVERT: J 1249 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8450 (t0) REVERT: J 1311 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7757 (ttmt) REVERT: L 110 LEU cc_start: 0.8644 (pp) cc_final: 0.8359 (mp) REVERT: L 322 MET cc_start: 0.3385 (mtt) cc_final: 0.2797 (ttp) REVERT: L 440 THR cc_start: 0.8141 (m) cc_final: 0.7712 (p) REVERT: L 476 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7925 (ptt-90) REVERT: L 538 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7545 (mp0) REVERT: M 262 LEU cc_start: 0.7543 (pt) cc_final: 0.6606 (pp) outliers start: 114 outliers final: 60 residues processed: 412 average time/residue: 0.6210 time to fit residues: 304.1042 Evaluate side-chains 386 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 311 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1211 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 321 LYS Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 599 LYS Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 394 TYR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain M residue 257 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 33 optimal weight: 7.9990 chunk 289 optimal weight: 30.0000 chunk 206 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 80 optimal weight: 0.0370 chunk 236 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 294 optimal weight: 8.9990 chunk 68 optimal weight: 30.0000 chunk 3 optimal weight: 4.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 18 GLN H 103 ASN ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J1238 GLN J1249 ASN L 396 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.206159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118434 restraints weight = 33636.470| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.52 r_work: 0.3114 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 31614 Z= 0.258 Angle : 0.664 19.166 43022 Z= 0.341 Chirality : 0.046 0.323 4944 Planarity : 0.005 0.057 5337 Dihedral : 13.885 179.487 5133 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.30 % Rotamer: Outliers : 3.95 % Allowed : 14.18 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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 (0.14), residues: 3721 helix: 1.40 (0.14), residues: 1494 sheet: -0.48 (0.24), residues: 429 loop : -1.28 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J1371 TYR 0.026 0.002 TYR G 177 PHE 0.018 0.002 PHE J 17 TRP 0.008 0.001 TRP I 807 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.26 (31606) covalent geometry : angle 0.65332 / 0.34 (43010) hydrogen bonds : bond 0.05219 / 3.58 ( 1372) hydrogen bonds : angle 4.42471 / 3.03 ( 3810) metal coordination : bond 0.01206 / 0.67 ( 8) metal coordination : angle 7.25712 / 4.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 330 time to evaluate : 1.131 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: G 95 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8154 (ptpp) REVERT: G 186 ASN cc_start: 0.8100 (m-40) cc_final: 0.7699 (p0) REVERT: H 79 LEU cc_start: 0.8232 (tt) cc_final: 0.7599 (mt) REVERT: H 176 CYS cc_start: 0.7968 (p) cc_final: 0.7725 (t) REVERT: I 28 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8727 (pp) REVERT: I 40 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: I 102 LEU cc_start: 0.7631 (tp) cc_final: 0.7389 (tp) REVERT: I 413 GLU cc_start: 0.7371 (mp0) cc_final: 0.6860 (mp0) REVERT: I 510 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: I 768 MET cc_start: 0.8827 (ptm) cc_final: 0.8334 (ptp) REVERT: I 779 ARG cc_start: 0.8514 (ttt-90) cc_final: 0.8001 (ttm170) REVERT: I 912 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6860 (p0) REVERT: I 940 GLU cc_start: 0.7640 (pp20) cc_final: 0.7326 (pp20) REVERT: I 943 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7662 (mtpm) REVERT: I 1028 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7516 (tttt) REVERT: I 1135 GLN cc_start: 0.8152 (mt0) cc_final: 0.7787 (mm110) REVERT: I 1140 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7748 (mtmt) REVERT: I 1211 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8098 (ptm160) REVERT: I 1269 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8528 (ttt-90) REVERT: J 60 ARG cc_start: 0.8567 (ptm-80) cc_final: 0.7641 (ptp90) REVERT: J 130 MET cc_start: 0.8309 (mtp) cc_final: 0.7938 (mtm) REVERT: J 155 GLU cc_start: 0.5715 (pm20) cc_final: 0.4870 (pm20) REVERT: J 158 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6253 (tt0) REVERT: J 334 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.4816 (tptt) REVERT: J 505 ASP cc_start: 0.7636 (t0) cc_final: 0.7140 (m-30) REVERT: J 652 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6943 (tt0) REVERT: J 663 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: J 875 ASN cc_start: 0.7409 (m-40) cc_final: 0.7121 (m110) REVERT: J 1236 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: J 1244 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7894 (mm-40) REVERT: J 1287 ILE cc_start: 0.7329 (pt) cc_final: 0.7073 (pp) REVERT: J 1311 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7800 (ttmt) REVERT: L 322 MET cc_start: 0.3643 (mtt) cc_final: 0.3071 (ttp) REVERT: L 413 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6426 (mtp) REVERT: L 476 ARG cc_start: 0.8324 (ttp-110) cc_final: 0.7998 (ptt-90) REVERT: L 513 ASP cc_start: 0.6441 (t0) cc_final: 0.6121 (t0) REVERT: M 262 LEU cc_start: 0.7665 (pt) cc_final: 0.6766 (pp) outliers start: 126 outliers final: 61 residues processed: 416 average time/residue: 0.5963 time to fit residues: 295.8191 Evaluate side-chains 389 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 316 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1211 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1269 ARG Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 399 LYS Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 394 TYR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain M residue 257 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 131 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 116 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 370 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 18 GLN H 103 ASN I 811 ASN J 777 HIS L 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.209373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120765 restraints weight = 33534.258| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.09 r_work: 0.3212 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31614 Z= 0.124 Angle : 0.568 13.177 43022 Z= 0.294 Chirality : 0.042 0.284 4944 Planarity : 0.004 0.058 5337 Dihedral : 13.757 179.521 5133 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 3.29 % Allowed : 15.31 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: 0.10 (0.14), residues: 3721 helix: 1.59 (0.14), residues: 1494 sheet: -0.39 (0.25), residues: 401 loop : -1.16 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J1371 TYR 0.026 0.001 TYR J 144 PHE 0.011 0.001 PHE J1319 TRP 0.008 0.001 TRP I 807 HIS 0.005 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (31606) covalent geometry : angle 0.56089 / 0.29 (43010) hydrogen bonds : bond 0.04057 / 2.79 ( 1372) hydrogen bonds : angle 4.23712 / 2.90 ( 3810) metal coordination : bond 0.00680 / 0.38 ( 8) metal coordination : angle 5.56098 / 3.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 336 time to evaluate : 1.118 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: G 95 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8195 (ptpp) REVERT: G 186 ASN cc_start: 0.7991 (m-40) cc_final: 0.7747 (p0) REVERT: H 79 LEU cc_start: 0.8100 (tt) cc_final: 0.7522 (mt) REVERT: I 28 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8637 (pp) REVERT: I 40 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: I 102 LEU cc_start: 0.7607 (tp) cc_final: 0.7388 (tp) REVERT: I 510 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: I 587 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8545 (mt) REVERT: I 768 MET cc_start: 0.8844 (ptm) cc_final: 0.8368 (ptp) REVERT: I 779 ARG cc_start: 0.8424 (ttt-90) cc_final: 0.7960 (ttm170) REVERT: I 912 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6723 (p0) REVERT: I 940 GLU cc_start: 0.7652 (pp20) cc_final: 0.7376 (pp20) REVERT: I 943 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7577 (mtpm) REVERT: I 1028 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7529 (tttt) REVERT: I 1082 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8070 (mp) REVERT: I 1135 GLN cc_start: 0.8085 (mt0) cc_final: 0.7778 (mm-40) REVERT: I 1140 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7715 (mtmt) REVERT: I 1211 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8025 (ptm160) REVERT: J 60 ARG cc_start: 0.8484 (ptm-80) cc_final: 0.7596 (ptp90) REVERT: J 83 VAL cc_start: 0.8782 (p) cc_final: 0.8419 (m) REVERT: J 130 MET cc_start: 0.8231 (mtp) cc_final: 0.7859 (mtm) REVERT: J 158 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6325 (tt0) REVERT: J 334 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.4879 (tptt) REVERT: J 505 ASP cc_start: 0.7355 (t0) cc_final: 0.6964 (m-30) REVERT: J 652 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6929 (tt0) REVERT: J 663 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: J 875 ASN cc_start: 0.7380 (m-40) cc_final: 0.7167 (m110) REVERT: J 1189 MET cc_start: 0.7684 (ptm) cc_final: 0.7107 (tmt) REVERT: J 1236 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: J 1244 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7993 (mm-40) REVERT: J 1248 ILE cc_start: 0.8570 (pt) cc_final: 0.8318 (mt) REVERT: J 1287 ILE cc_start: 0.7317 (pt) cc_final: 0.7072 (pp) REVERT: J 1310 THR cc_start: 0.8959 (t) cc_final: 0.8743 (t) REVERT: J 1311 LYS cc_start: 0.8172 (ttmm) cc_final: 0.7754 (ttmt) REVERT: L 100 MET cc_start: 0.7113 (mtm) cc_final: 0.6710 (mtm) REVERT: L 110 LEU cc_start: 0.8614 (pp) cc_final: 0.8288 (mp) REVERT: L 288 MET cc_start: 0.7479 (mmm) cc_final: 0.7228 (mmm) REVERT: L 322 MET cc_start: 0.3620 (mtt) cc_final: 0.3068 (ttp) REVERT: L 409 ASN cc_start: 0.7851 (m-40) cc_final: 0.7619 (m110) REVERT: L 413 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6445 (mtp) REVERT: L 440 THR cc_start: 0.8163 (m) cc_final: 0.7734 (p) REVERT: L 470 MET cc_start: 0.8203 (ttm) cc_final: 0.7924 (mtt) REVERT: L 476 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7883 (ptt-90) REVERT: L 513 ASP cc_start: 0.6226 (t0) cc_final: 0.6008 (t0) REVERT: M 262 LEU cc_start: 0.7513 (pt) cc_final: 0.6605 (pp) outliers start: 105 outliers final: 52 residues processed: 413 average time/residue: 0.5869 time to fit residues: 289.9833 Evaluate side-chains 379 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 314 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1211 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 394 TYR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain M residue 257 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 72 optimal weight: 0.2980 chunk 195 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 184 optimal weight: 0.0370 chunk 83 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 165 optimal weight: 0.1980 chunk 146 optimal weight: 8.9990 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN I 628 HIS I 649 GLN I 811 ASN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J 865 HIS J1249 ASN L 396 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.211161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123423 restraints weight = 33696.111| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.24 r_work: 0.3229 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31614 Z= 0.106 Angle : 0.540 9.971 43022 Z= 0.281 Chirality : 0.041 0.277 4944 Planarity : 0.004 0.058 5337 Dihedral : 13.629 179.425 5132 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.03 % Rotamer: Outliers : 2.60 % Allowed : 16.35 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: 0.28 (0.14), residues: 3721 helix: 1.78 (0.14), residues: 1492 sheet: -0.32 (0.25), residues: 396 loop : -1.07 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J1371 TYR 0.021 0.001 TYR J 144 PHE 0.011 0.001 PHE J1319 TRP 0.007 0.001 TRP J 868 HIS 0.006 0.000 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (31606) covalent geometry : angle 0.53550 / 0.28 (43010) hydrogen bonds : bond 0.03595 / 2.48 ( 1372) hydrogen bonds : angle 4.09014 / 2.80 ( 3810) metal coordination : bond 0.00550 / 0.29 ( 8) metal coordination : angle 4.42244 / 3.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 335 time to evaluate : 1.116 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: G 33 ARG cc_start: 0.8022 (mmm-85) cc_final: 0.7811 (tpm170) REVERT: G 95 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8184 (ptpp) REVERT: H 79 LEU cc_start: 0.7981 (tt) cc_final: 0.7487 (mt) REVERT: H 172 LEU cc_start: 0.8926 (mt) cc_final: 0.8670 (mt) REVERT: I 28 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8593 (pp) REVERT: I 40 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: I 102 LEU cc_start: 0.7572 (tp) cc_final: 0.7359 (tp) REVERT: I 203 LYS cc_start: 0.8026 (mtpm) cc_final: 0.7765 (mtpm) REVERT: I 510 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: I 587 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8434 (mt) REVERT: I 768 MET cc_start: 0.8867 (ptm) cc_final: 0.8379 (ptp) REVERT: I 779 ARG cc_start: 0.8420 (ttt-90) cc_final: 0.7939 (ttm170) REVERT: I 876 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8029 (mm-30) REVERT: I 912 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6622 (p0) REVERT: I 940 GLU cc_start: 0.7667 (pp20) cc_final: 0.7407 (pp20) REVERT: I 1028 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7558 (tttt) REVERT: I 1082 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8062 (mp) REVERT: I 1140 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7868 (mmtt) REVERT: I 1211 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8011 (ptm160) REVERT: J 29 MET cc_start: 0.7909 (tpp) cc_final: 0.7661 (tpt) REVERT: J 60 ARG cc_start: 0.8464 (ptm-80) cc_final: 0.7467 (ptp90) REVERT: J 83 VAL cc_start: 0.8766 (p) cc_final: 0.8393 (m) REVERT: J 130 MET cc_start: 0.8170 (mtp) cc_final: 0.7928 (mtm) REVERT: J 505 ASP cc_start: 0.7282 (t0) cc_final: 0.6846 (m-30) REVERT: J 652 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6902 (tt0) REVERT: J 663 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: J 875 ASN cc_start: 0.7363 (m-40) cc_final: 0.7108 (m110) REVERT: J 1189 MET cc_start: 0.7648 (ptm) cc_final: 0.7083 (tmt) REVERT: J 1236 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: J 1244 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7685 (mp10) REVERT: J 1287 ILE cc_start: 0.7244 (pt) cc_final: 0.6979 (pp) REVERT: J 1311 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7714 (ttmt) REVERT: L 100 MET cc_start: 0.7035 (mtm) cc_final: 0.6717 (mtm) REVERT: L 110 LEU cc_start: 0.8622 (pp) cc_final: 0.8286 (mp) REVERT: L 409 ASN cc_start: 0.7849 (m-40) cc_final: 0.7609 (m110) REVERT: L 413 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6361 (mtp) REVERT: L 440 THR cc_start: 0.8089 (m) cc_final: 0.7664 (p) REVERT: L 470 MET cc_start: 0.8168 (ttm) cc_final: 0.7941 (mtt) REVERT: L 509 THR cc_start: 0.8019 (t) cc_final: 0.7060 (m) REVERT: L 611 LEU cc_start: 0.8490 (tt) cc_final: 0.8110 (pp) REVERT: M 262 LEU cc_start: 0.7582 (pt) cc_final: 0.6675 (pp) outliers start: 83 outliers final: 43 residues processed: 397 average time/residue: 0.6153 time to fit residues: 292.0713 Evaluate side-chains 370 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 316 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1211 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 144 TYR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 394 TYR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain M residue 257 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 268 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 153 optimal weight: 0.0770 chunk 118 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 372 optimal weight: 80.0000 chunk 171 optimal weight: 1.9990 chunk 363 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN I 582 ASN I 628 HIS I 649 GLN I 811 ASN J 430 HIS J 777 HIS J 865 HIS J1249 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.209276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120007 restraints weight = 33639.687| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.97 r_work: 0.3225 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31614 Z= 0.144 Angle : 0.575 10.436 43022 Z= 0.298 Chirality : 0.042 0.294 4944 Planarity : 0.004 0.074 5337 Dihedral : 13.633 179.371 5129 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 2.35 % Allowed : 17.07 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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 (0.14), residues: 3721 helix: 1.71 (0.14), residues: 1496 sheet: -0.22 (0.25), residues: 412 loop : -1.12 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J1371 TYR 0.020 0.001 TYR J 144 PHE 0.012 0.001 PHE J1319 TRP 0.007 0.001 TRP L 326 HIS 0.006 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (31606) covalent geometry : angle 0.57044 / 0.30 (43010) hydrogen bonds : bond 0.03996 / 2.76 ( 1372) hydrogen bonds : angle 4.09853 / 2.81 ( 3810) metal coordination : bond 0.00710 / 0.38 ( 8) metal coordination : angle 4.22811 / 2.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 320 time to evaluate : 1.139 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: G 95 LYS cc_start: 0.8489 (mtmm) cc_final: 0.8178 (ptpp) REVERT: H 79 LEU cc_start: 0.7973 (tt) cc_final: 0.7467 (mt) REVERT: H 172 LEU cc_start: 0.8961 (mt) cc_final: 0.8675 (mt) REVERT: I 28 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8598 (pp) REVERT: I 40 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: I 102 LEU cc_start: 0.7584 (tp) cc_final: 0.7348 (tp) REVERT: I 203 LYS cc_start: 0.8039 (mtpm) cc_final: 0.7785 (mtpm) REVERT: I 413 GLU cc_start: 0.7398 (mp0) cc_final: 0.6890 (mp0) REVERT: I 510 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: I 587 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8546 (mt) REVERT: I 768 MET cc_start: 0.8877 (ptm) cc_final: 0.8397 (ptp) REVERT: I 779 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.7976 (ttm170) REVERT: I 912 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6621 (p0) REVERT: I 940 GLU cc_start: 0.7681 (pp20) cc_final: 0.7403 (pp20) REVERT: I 1028 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7513 (tttt) REVERT: I 1082 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8093 (mp) REVERT: I 1135 GLN cc_start: 0.8132 (mt0) cc_final: 0.7782 (mm110) REVERT: I 1211 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8060 (ptm160) REVERT: J 29 MET cc_start: 0.7964 (tpp) cc_final: 0.7712 (tpt) REVERT: J 60 ARG cc_start: 0.8446 (ptm-80) cc_final: 0.7529 (ptp90) REVERT: J 83 VAL cc_start: 0.8806 (p) cc_final: 0.8436 (m) REVERT: J 155 GLU cc_start: 0.5475 (pm20) cc_final: 0.5101 (pm20) REVERT: J 158 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.6507 (tt0) REVERT: J 505 ASP cc_start: 0.7309 (t0) cc_final: 0.6848 (m-30) REVERT: J 652 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6925 (tt0) REVERT: J 663 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: J 875 ASN cc_start: 0.7405 (m-40) cc_final: 0.7134 (m110) REVERT: J 1025 MET cc_start: 0.5796 (mpm) cc_final: 0.4219 (ppp) REVERT: J 1189 MET cc_start: 0.7600 (ptm) cc_final: 0.7040 (tmt) REVERT: J 1236 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: J 1244 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7728 (mp10) REVERT: J 1249 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8415 (t0) REVERT: J 1311 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7730 (ttmt) REVERT: L 100 MET cc_start: 0.7075 (mtm) cc_final: 0.6780 (mtm) REVERT: L 409 ASN cc_start: 0.7883 (m-40) cc_final: 0.7646 (m110) REVERT: L 413 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6667 (mtp) REVERT: L 440 THR cc_start: 0.8127 (m) cc_final: 0.7688 (p) REVERT: L 470 MET cc_start: 0.8183 (ttm) cc_final: 0.7947 (mtt) REVERT: L 611 LEU cc_start: 0.8485 (tt) cc_final: 0.8116 (pp) REVERT: M 262 LEU cc_start: 0.7481 (pt) cc_final: 0.6557 (pp) outliers start: 75 outliers final: 44 residues processed: 374 average time/residue: 0.6312 time to fit residues: 281.4691 Evaluate side-chains 364 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 308 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1211 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 394 TYR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 141 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 297 optimal weight: 0.5980 chunk 219 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 328 optimal weight: 2.9990 chunk 287 optimal weight: 0.9980 chunk 363 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN I 628 HIS I 811 ASN J 430 HIS J 777 HIS J 865 HIS L 396 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.209816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120747 restraints weight = 33736.841| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.00 r_work: 0.3231 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31614 Z= 0.127 Angle : 0.579 14.297 43022 Z= 0.296 Chirality : 0.042 0.371 4944 Planarity : 0.004 0.062 5337 Dihedral : 13.623 179.307 5129 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 2.17 % Allowed : 17.29 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: 0.27 (0.14), residues: 3721 helix: 1.75 (0.14), residues: 1496 sheet: -0.19 (0.25), residues: 406 loop : -1.11 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J1371 TYR 0.022 0.001 TYR J 144 PHE 0.011 0.001 PHE J1319 TRP 0.007 0.001 TRP I 807 HIS 0.006 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (31606) covalent geometry : angle 0.57480 / 0.30 (43010) hydrogen bonds : bond 0.03817 / 2.64 ( 1372) hydrogen bonds : angle 4.08068 / 2.79 ( 3810) metal coordination : bond 0.00620 / 0.33 ( 8) metal coordination : angle 4.03550 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 316 time to evaluate : 1.135 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: G 33 ARG cc_start: 0.7992 (mmm-85) cc_final: 0.7766 (tpm170) REVERT: G 95 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8169 (ptpp) REVERT: H 79 LEU cc_start: 0.7978 (tt) cc_final: 0.7500 (mt) REVERT: H 172 LEU cc_start: 0.8986 (mt) cc_final: 0.8714 (mt) REVERT: I 28 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8581 (pp) REVERT: I 40 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: I 203 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7801 (mtpm) REVERT: I 413 GLU cc_start: 0.7436 (mp0) cc_final: 0.6919 (mp0) REVERT: I 488 MET cc_start: 0.7043 (mmm) cc_final: 0.6770 (mmt) REVERT: I 510 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: I 587 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8676 (mt) REVERT: I 768 MET cc_start: 0.8864 (ptm) cc_final: 0.8384 (ptp) REVERT: I 779 ARG cc_start: 0.8451 (ttt-90) cc_final: 0.7987 (ttm170) REVERT: I 912 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6631 (p0) REVERT: I 940 GLU cc_start: 0.7669 (pp20) cc_final: 0.7414 (pp20) REVERT: I 1028 LYS cc_start: 0.7775 (ttpt) cc_final: 0.7495 (tttt) REVERT: I 1082 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8102 (mp) REVERT: I 1135 GLN cc_start: 0.8140 (mt0) cc_final: 0.7790 (mm110) REVERT: I 1211 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8026 (ptm160) REVERT: J 29 MET cc_start: 0.7931 (tpp) cc_final: 0.7682 (tpt) REVERT: J 60 ARG cc_start: 0.8460 (ptm-80) cc_final: 0.7510 (ptp90) REVERT: J 83 VAL cc_start: 0.8820 (p) cc_final: 0.8446 (m) REVERT: J 126 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7597 (mp) REVERT: J 155 GLU cc_start: 0.5523 (pm20) cc_final: 0.5310 (pm20) REVERT: J 158 GLN cc_start: 0.6847 (OUTLIER) cc_final: 0.6549 (tt0) REVERT: J 505 ASP cc_start: 0.7299 (t0) cc_final: 0.6880 (m-30) REVERT: J 652 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6929 (tt0) REVERT: J 663 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: J 875 ASN cc_start: 0.7332 (m-40) cc_final: 0.7086 (m110) REVERT: J 1025 MET cc_start: 0.6055 (mpm) cc_final: 0.4487 (ppp) REVERT: J 1189 MET cc_start: 0.7661 (ptm) cc_final: 0.7055 (tmt) REVERT: J 1236 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: J 1244 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7687 (mp10) REVERT: J 1311 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7715 (ttmt) REVERT: L 100 MET cc_start: 0.7062 (mtm) cc_final: 0.6773 (mtm) REVERT: L 110 LEU cc_start: 0.8613 (pp) cc_final: 0.8278 (mp) REVERT: L 131 GLN cc_start: 0.9399 (pt0) cc_final: 0.9169 (pp30) REVERT: L 276 MET cc_start: 0.8321 (tmm) cc_final: 0.8052 (ppp) REVERT: L 409 ASN cc_start: 0.7842 (m-40) cc_final: 0.7617 (m110) REVERT: L 413 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6631 (mtp) REVERT: L 440 THR cc_start: 0.8119 (m) cc_final: 0.7677 (p) REVERT: L 470 MET cc_start: 0.8213 (ttm) cc_final: 0.7987 (mtt) REVERT: L 611 LEU cc_start: 0.8477 (tt) cc_final: 0.8154 (pp) REVERT: M 262 LEU cc_start: 0.7438 (pt) cc_final: 0.6552 (pp) outliers start: 69 outliers final: 44 residues processed: 367 average time/residue: 0.5914 time to fit residues: 259.2809 Evaluate side-chains 371 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 314 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1211 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 394 TYR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 226 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 350 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 326 optimal weight: 40.0000 chunk 262 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN I 628 HIS I 811 ASN I 834 GLN I 932 GLN J 777 HIS J 865 HIS L 362 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.206066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117596 restraints weight = 33533.028| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.44 r_work: 0.3128 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 31614 Z= 0.256 Angle : 0.680 13.984 43022 Z= 0.347 Chirality : 0.047 0.328 4944 Planarity : 0.005 0.066 5337 Dihedral : 13.734 179.084 5129 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 2.29 % Allowed : 17.04 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: -0.03 (0.14), residues: 3721 helix: 1.48 (0.14), residues: 1495 sheet: -0.37 (0.25), residues: 423 loop : -1.26 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J1371 TYR 0.027 0.002 TYR G 177 PHE 0.018 0.002 PHE J 17 TRP 0.013 0.002 TRP J 868 HIS 0.006 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.26 (31606) covalent geometry : angle 0.67427 / 0.35 (43010) hydrogen bonds : bond 0.05072 / 3.50 ( 1372) hydrogen bonds : angle 4.28660 / 2.93 ( 3810) metal coordination : bond 0.01108 / 0.61 ( 8) metal coordination : angle 5.11423 / 3.50 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 329 time to evaluate : 1.028 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: G 95 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8112 (ptpp) REVERT: H 79 LEU cc_start: 0.8129 (tt) cc_final: 0.7549 (mt) REVERT: H 172 LEU cc_start: 0.9046 (mt) cc_final: 0.8713 (mt) REVERT: H 176 CYS cc_start: 0.8016 (p) cc_final: 0.7727 (t) REVERT: I 28 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8683 (pp) REVERT: I 40 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: I 203 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7871 (mtpm) REVERT: I 413 GLU cc_start: 0.7458 (mp0) cc_final: 0.6958 (mp0) REVERT: I 488 MET cc_start: 0.6913 (mmm) cc_final: 0.6639 (mmt) REVERT: I 510 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: I 745 GLU cc_start: 0.7666 (pt0) cc_final: 0.7465 (pp20) REVERT: I 768 MET cc_start: 0.8842 (ptm) cc_final: 0.8351 (ptp) REVERT: I 779 ARG cc_start: 0.8528 (ttt-90) cc_final: 0.7976 (ttm170) REVERT: I 912 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6687 (p0) REVERT: I 940 GLU cc_start: 0.7683 (pp20) cc_final: 0.7398 (pp20) REVERT: I 943 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7657 (mtpm) REVERT: I 1028 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7412 (tttt) REVERT: I 1135 GLN cc_start: 0.8277 (mt0) cc_final: 0.8004 (mm-40) REVERT: I 1188 ASP cc_start: 0.8132 (t0) cc_final: 0.7736 (t0) REVERT: I 1211 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8116 (ptm160) REVERT: J 60 ARG cc_start: 0.8497 (ptm-80) cc_final: 0.7583 (ptp90) REVERT: J 155 GLU cc_start: 0.5535 (pm20) cc_final: 0.5201 (pm20) REVERT: J 158 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6468 (tt0) REVERT: J 505 ASP cc_start: 0.7720 (t0) cc_final: 0.7246 (m-30) REVERT: J 652 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6961 (tt0) REVERT: J 663 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: J 875 ASN cc_start: 0.7440 (m-40) cc_final: 0.7107 (m110) REVERT: J 1025 MET cc_start: 0.6129 (mpm) cc_final: 0.4508 (ppp) REVERT: J 1189 MET cc_start: 0.7670 (ptm) cc_final: 0.7043 (tmt) REVERT: J 1244 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8030 (mm-40) REVERT: J 1287 ILE cc_start: 0.7199 (pt) cc_final: 0.6961 (pp) REVERT: J 1311 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7757 (ttmt) REVERT: L 131 GLN cc_start: 0.9427 (pt0) cc_final: 0.9183 (pp30) REVERT: L 409 ASN cc_start: 0.7878 (m-40) cc_final: 0.7631 (m110) REVERT: L 413 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6682 (mtp) REVERT: L 440 THR cc_start: 0.8167 (m) cc_final: 0.7703 (p) REVERT: L 611 LEU cc_start: 0.8567 (tt) cc_final: 0.8142 (pp) REVERT: M 262 LEU cc_start: 0.7516 (pt) cc_final: 0.6640 (pp) outliers start: 73 outliers final: 48 residues processed: 384 average time/residue: 0.6350 time to fit residues: 290.6320 Evaluate side-chains 372 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1211 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 394 TYR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 182 optimal weight: 0.1980 chunk 311 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 340 optimal weight: 40.0000 chunk 50 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 18 GLN H 103 ASN I 628 HIS J 777 HIS J 865 HIS J1249 ASN L 362 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.206445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116446 restraints weight = 33584.993| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.97 r_work: 0.3159 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 31614 Z= 0.226 Angle : 0.776 59.200 43022 Z= 0.419 Chirality : 0.045 0.611 4944 Planarity : 0.005 0.064 5337 Dihedral : 13.749 179.074 5129 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 2.13 % Allowed : 17.29 % Favored : 80.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3721 helix: 1.47 (0.14), residues: 1500 sheet: -0.39 (0.24), residues: 423 loop : -1.27 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J1371 TYR 0.026 0.002 TYR G 177 PHE 0.017 0.002 PHE J 17 TRP 0.012 0.001 TRP J 868 HIS 0.006 0.001 HIS I 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (31606) covalent geometry : angle 0.77138 / 0.42 (43010) hydrogen bonds : bond 0.04855 / 3.35 ( 1372) hydrogen bonds : angle 4.29628 / 2.93 ( 3810) metal coordination : bond 0.01007 / 0.53 ( 8) metal coordination : angle 5.12985 / 3.52 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14189.29 seconds wall clock time: 240 minutes 51.80 seconds (14451.80 seconds total)