Starting phenix.real_space_refine on Fri Mar 6 16:17:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psr_20461/03_2026/6psr_20461_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psr_20461/03_2026/6psr_20461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6psr_20461/03_2026/6psr_20461_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psr_20461/03_2026/6psr_20461_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6psr_20461/03_2026/6psr_20461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psr_20461/03_2026/6psr_20461.map" } resolution = 3.4 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= 0.000 sd= 0.007 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 3 6.06 5 P 71 5.49 5 Mg 1 5.21 5 S 140 5.16 5 C 19980 2.51 5 N 5669 2.21 5 O 6322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 186 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32186 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 220} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10559 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 54, 'TRANS': 1280} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 10466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10466 Classifications: {'peptide': 1345} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1286} Chain breaks: 2 Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 71} Chain: "L" Number of atoms: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4407 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 530} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 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: "N" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 746 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "P" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 710 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 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 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14457 SG CYS J 70 73.573 103.420 112.606 1.00 39.52 S ATOM 14471 SG CYS J 72 74.095 106.922 113.235 1.00 49.13 S ATOM 14579 SG CYS J 85 72.419 104.098 115.733 1.00 46.00 S ATOM 14603 SG CYS J 88 70.818 105.252 111.826 1.00 54.96 S ATOM 20291 SG CYS J 814 67.496 41.455 88.288 1.00 26.97 S ATOM 20856 SG CYS J 888 67.619 44.786 87.200 1.00 23.51 S ATOM 20907 SG CYS J 895 71.400 42.779 87.449 1.00 19.60 S ATOM 20928 SG CYS J 898 68.946 41.871 85.150 1.00 15.61 S ATOM 30334 SG CYS N 37 49.053 53.838 27.455 1.00 53.35 S ATOM 30354 SG CYS N 40 47.725 55.372 24.343 1.00 64.59 S ATOM 30491 SG CYS N 58 50.591 57.228 24.695 1.00 45.82 S ATOM 30513 SG CYS N 61 48.150 57.408 27.245 1.00 49.24 S Time building chain proxies: 7.16, per 1000 atoms: 0.22 Number of scatterers: 32186 At special positions: 0 Unit cell: (154.7, 152.1, 163.8, 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 3 29.99 S 140 16.00 P 71 15.00 Mg 1 11.99 O 6322 8.00 N 5669 7.00 C 19980 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: 3.13 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " 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 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " Number of angles added : 18 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7254 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 49 sheets defined 43.1% alpha, 12.1% beta 33 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.852A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 232 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.865A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 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: 4.195A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 removed outlier: 3.705A pdb=" N LYS I 8 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.678A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 88 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.677A pdb=" N SER I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 163 through 167' Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.946A 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 243 through 247 Processing helix chain 'I' and resid 270 through 280 removed outlier: 3.625A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.548A pdb=" N TYR I 291 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.587A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 387 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 4.610A pdb=" N GLU I 461 " --> pdb=" O GLY I 457 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 519 through 527 removed outlier: 3.651A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.656A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 613 removed outlier: 4.076A pdb=" N GLY I 612 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 656 through 660 removed outlier: 3.515A pdb=" N GLN I 659 " --> pdb=" O SER I 656 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 656 through 660' Processing helix chain 'I' and resid 663 through 667 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 703 through 712 removed outlier: 4.577A pdb=" N ALA I 707 " --> pdb=" O GLY I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 898 through 906 removed outlier: 3.615A pdb=" N PHE I 906 " --> pdb=" O LEU I 902 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 removed outlier: 3.766A pdb=" N LEU I 946 " --> pdb=" O ASP I 942 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU I 947 " --> pdb=" O LYS I 943 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE I 948 " --> pdb=" O ARG I 944 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU I 949 " --> pdb=" O ALA I 945 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET I 951 " --> pdb=" O GLU I 947 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.797A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1100 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.534A pdb=" N GLY I1125 " --> pdb=" O ALA I1121 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE I1128 " --> pdb=" O ILE I1124 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.578A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.631A pdb=" N LEU I1172 " --> pdb=" O GLU I1168 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.920A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS I1306 " --> pdb=" O THR I1302 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.514A pdb=" N GLU J 100 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 117 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.656A pdb=" N TYR J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 192 Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 237 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 284 removed outlier: 4.203A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 309 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.940A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU J 376 " --> pdb=" O MET J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 417 removed outlier: 3.689A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (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 478 Processing helix chain 'J' and resid 478 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.672A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.707A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 613 removed outlier: 3.534A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.797A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.353A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 729 removed outlier: 3.619A pdb=" N GLY J 729 " --> pdb=" O MET J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.008A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 789 removed outlier: 4.034A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 794 through 804 removed outlier: 3.518A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.789A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.552A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1138 through 1147 removed outlier: 3.829A pdb=" N LEU J1144 " --> pdb=" O ARG J1140 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J1147 " --> pdb=" O ASP J1143 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.154A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.439A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1318 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1351 removed outlier: 3.562A pdb=" N VAL J1351 " --> pdb=" O LEU J1347 " (cutoff:3.500A) Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 14 removed outlier: 3.661A pdb=" N GLU K 11 " --> pdb=" O GLN K 7 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS K 12 " --> pdb=" O ASP K 8 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.610A 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 75 Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 24 through 31 Processing helix chain 'L' and resid 37 through 52 removed outlier: 3.512A pdb=" N GLY L 52 " --> pdb=" O ILE L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 removed outlier: 3.589A pdb=" N ALA L 79 " --> pdb=" O ASP L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 107 Processing helix chain 'L' and resid 115 through 136 Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 214 through 234 Processing helix chain 'L' and resid 244 through 257 removed outlier: 3.542A pdb=" N GLU L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 292 removed outlier: 3.966A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 removed outlier: 3.622A pdb=" N PHE L 302 " --> pdb=" O PRO L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 323 removed outlier: 4.054A pdb=" N ASN L 323 " --> pdb=" O ILE L 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 392 removed outlier: 3.636A pdb=" N VAL L 358 " --> pdb=" O THR L 354 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU L 378 " --> pdb=" O ARG L 374 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS L 392 " --> pdb=" O ILE L 388 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 395 No H-bonds generated for 'chain 'L' and resid 393 through 395' Processing helix chain 'L' and resid 400 through 417 Processing helix chain 'L' and resid 426 through 447 removed outlier: 4.122A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.634A pdb=" N GLN L 469 " --> pdb=" O ARG L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 492 through 501 Processing helix chain 'L' and resid 518 through 522 removed outlier: 3.717A pdb=" N PHE L 522 " --> pdb=" O LEU L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 534 through 550 removed outlier: 3.660A pdb=" N SER L 539 " --> pdb=" O ALA L 535 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.920A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 609 Processing helix chain 'M' and resid 250 through 255 removed outlier: 4.080A pdb=" N ARG M 255 " --> pdb=" O ILE M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 273 Processing helix chain 'M' and resid 277 through 282 Processing helix chain 'M' and resid 285 through 291 Processing helix chain 'M' and resid 296 through 310 removed outlier: 3.896A pdb=" N LEU M 300 " --> pdb=" O GLY M 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 27 removed outlier: 3.584A pdb=" N GLU N 7 " --> pdb=" O ASP N 3 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA N 8 " --> pdb=" O GLU N 4 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR N 9 " --> pdb=" O ALA N 5 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE N 27 " --> pdb=" O ILE N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 52 Processing helix chain 'N' and resid 58 through 71 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 8.571A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR G 27 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (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 97 through 105 removed outlier: 7.323A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.775A 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: 3.664A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 16 through 18 removed outlier: 6.292A pdb=" N HIS H 23 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N THR H 207 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP H 199 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 53 through 61 removed outlier: 4.988A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.449A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 66 through 75 removed outlier: 6.918A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET I 124 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 453 removed outlier: 6.356A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'I' and resid 195 through 196 Processing sheet with id=AB8, first strand: chain 'I' and resid 284 through 285 removed outlier: 4.539A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.411A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) 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 633 through 637 Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.575A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.707A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (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 1209 through 1210 removed outlier: 6.997A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.575A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD1, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'I' and resid 1087 through 1088 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 Processing sheet with id=AD5, first strand: chain 'I' and resid 1336 through 1339 Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.523A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (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 253 Processing sheet with id=AD9, first strand: chain 'J' and resid 491 through 492 removed outlier: 5.015A pdb=" N GLU J 497 " --> pdb=" O SER J 492 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE2, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE3, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE4, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'J' and resid 957 through 961 Processing sheet with id=AE6, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE7, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.766A pdb=" N VAL J1113 " --> pdb=" O VAL J1035 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1051 removed outlier: 3.526A pdb=" N LEU J1056 " --> pdb=" O ASP J1051 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1089 through 1090 removed outlier: 3.646A pdb=" N ILE J1090 " --> pdb=" O THR J1093 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1106 through 1107 Processing sheet with id=AF2, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 Processing sheet with id=AF4, first strand: chain 'L' and resid 22 through 23 removed outlier: 6.051A pdb=" N LEU L 22 " --> pdb=" O MET L 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 1328 hydrogen bonds defined for protein. 3726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10704 1.34 - 1.46: 6910 1.46 - 1.59: 14790 1.59 - 1.71: 156 1.71 - 1.84: 252 Bond restraints: 32812 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.836 -0.304 2.00e-02 2.50e+03 2.30e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.816 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C19 1N7 J1505 " pdb=" C3 1N7 J1505 " ideal model delta sigma weight residual 1.532 1.814 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.730 -0.198 2.00e-02 2.50e+03 9.77e+01 ... (remaining 32807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 43402 2.29 - 4.58: 1094 4.58 - 6.88: 111 6.88 - 9.17: 24 9.17 - 11.46: 6 Bond angle restraints: 44637 Sorted by residual: angle pdb=" N LYS I 9 " pdb=" CA LYS I 9 " pdb=" C LYS I 9 " ideal model delta sigma weight residual 112.72 104.78 7.94 1.28e+00 6.10e-01 3.84e+01 angle pdb=" C ARG J 53 " pdb=" N ASP J 54 " pdb=" CA ASP J 54 " ideal model delta sigma weight residual 121.54 133.00 -11.46 1.91e+00 2.74e-01 3.60e+01 angle pdb=" N VAL J 839 " pdb=" CA VAL J 839 " pdb=" C VAL J 839 " ideal model delta sigma weight residual 113.10 107.37 5.73 9.70e-01 1.06e+00 3.49e+01 angle pdb=" N GLY I 162 " pdb=" CA GLY I 162 " pdb=" C GLY I 162 " ideal model delta sigma weight residual 111.67 116.93 -5.26 9.20e-01 1.18e+00 3.27e+01 angle pdb=" C PHE I 15 " pdb=" N GLY I 16 " pdb=" CA GLY I 16 " ideal model delta sigma weight residual 121.41 111.61 9.80 1.96e+00 2.60e-01 2.50e+01 ... (remaining 44632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 19049 34.25 - 68.51: 1163 68.51 - 102.76: 68 102.76 - 137.02: 3 137.02 - 171.27: 3 Dihedral angle restraints: 20286 sinusoidal: 9041 harmonic: 11245 Sorted by residual: dihedral pdb=" CA ARG J 53 " pdb=" C ARG J 53 " pdb=" N ASP J 54 " pdb=" CA ASP J 54 " ideal model delta harmonic sigma weight residual 180.00 45.18 134.82 0 5.00e+00 4.00e-02 7.27e+02 dihedral pdb=" CA PRO I 897 " pdb=" C PRO I 897 " pdb=" N GLU I 898 " pdb=" CA GLU I 898 " ideal model delta harmonic sigma weight residual -180.00 -145.58 -34.42 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CA ASN I 519 " pdb=" C ASN I 519 " pdb=" N PRO I 520 " pdb=" CA PRO I 520 " ideal model delta harmonic sigma weight residual 180.00 149.35 30.65 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 20283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4497 0.072 - 0.145: 591 0.145 - 0.217: 32 0.217 - 0.290: 3 0.290 - 0.362: 2 Chirality restraints: 5125 Sorted by residual: 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 -2.90 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA GLN I 517 " pdb=" N GLN I 517 " pdb=" C GLN I 517 " pdb=" CB GLN I 517 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C15 1N7 L 701 " pdb=" C14 1N7 L 701 " pdb=" C16 1N7 L 701 " pdb=" C2 1N7 L 701 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 5122 not shown) Planarity restraints: 5564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I1223 " -0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO I1224 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO I1224 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO I1224 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO J 851 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA J1359 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C ALA J1359 " -0.036 2.00e-02 2.50e+03 pdb=" O ALA J1359 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY J1360 " 0.012 2.00e-02 2.50e+03 ... (remaining 5561 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 9 2.11 - 2.81: 9527 2.81 - 3.50: 45682 3.50 - 4.20: 77891 4.20 - 4.90: 135190 Nonbonded interactions: 268299 Sorted by model distance: nonbonded pdb=" O GLU L 146 " pdb=" OD1 ASP L 149 " model vdw 1.411 3.040 nonbonded pdb=" C GLU L 146 " pdb=" OD1 ASP L 149 " model vdw 1.982 3.270 nonbonded pdb=" OD1 ASP I 826 " pdb=" OG1 THR I 829 " model vdw 2.025 3.040 nonbonded pdb=" O LEU L 386 " pdb=" OG SER L 389 " model vdw 2.035 3.040 nonbonded pdb=" OG1 THR J 844 " pdb=" O ARG J 860 " model vdw 2.049 3.040 ... (remaining 268294 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 or (resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 158 or resid 171 through 233 or (resid 234 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 5 through 192 or (resid 193 and (name N or name CA or name \ C or name O or name CB )) or resid 194 through 228 or (resid 229 through 230 an \ d (name N or name CA or name C or name O or name CB )) or resid 231 through 232 \ or (resid 233 through 234 and (name N or name CA or name C or name O or name CB \ )))) } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.580 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.009 0.304 32824 Z= 0.429 Angle : 0.957 46.857 44655 Z= 0.517 Chirality : 0.048 0.362 5125 Planarity : 0.005 0.074 5564 Dihedral : 19.814 171.270 13032 Min Nonbonded Distance : 1.411 Molprobity Statistics. All-atom Clashscore : 37.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.33 % Favored : 89.60 % Rotamer: Outliers : 10.51 % Allowed : 21.45 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.05 % 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: -4.05 (0.11), residues: 3874 helix: -2.26 (0.10), residues: 1552 sheet: -3.30 (0.22), residues: 372 loop : -2.93 (0.12), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 538 TYR 0.022 0.002 TYR J 631 PHE 0.018 0.002 PHE J 377 TRP 0.025 0.002 TRP L 315 HIS 0.010 0.002 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00917 (32812) covalent geometry : angle 0.88862 (44637) hydrogen bonds : bond 0.15173 ( 1406) hydrogen bonds : angle 6.89383 ( 3886) metal coordination : bond 0.05690 ( 12) metal coordination : angle 17.76949 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 350 poor density : 526 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6628 (ttp-110) REVERT: G 160 HIS cc_start: 0.5019 (OUTLIER) cc_final: 0.4008 (p-80) REVERT: G 181 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6355 (mm-30) REVERT: H 51 MET cc_start: 0.7296 (mmm) cc_final: 0.6947 (tpt) REVERT: H 102 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6517 (tt) REVERT: I 20 GLN cc_start: 0.7044 (mm-40) cc_final: 0.6654 (mm-40) REVERT: I 301 TYR cc_start: 0.5241 (OUTLIER) cc_final: 0.4919 (m-10) REVERT: I 407 ARG cc_start: 0.6959 (tpp80) cc_final: 0.6755 (mtp180) REVERT: I 422 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7466 (mmtt) REVERT: I 478 ARG cc_start: 0.6597 (tmt-80) cc_final: 0.6223 (tpt90) REVERT: I 800 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8046 (mtp) REVERT: I 951 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7456 (ttp) REVERT: I 990 ASP cc_start: 0.5370 (OUTLIER) cc_final: 0.5121 (p0) REVERT: I 1301 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7924 (ptt90) REVERT: J 87 LYS cc_start: 0.6843 (tppt) cc_final: 0.6611 (ttpt) REVERT: J 129 ASP cc_start: 0.6381 (OUTLIER) cc_final: 0.5839 (t70) REVERT: J 133 ARG cc_start: 0.7083 (tpt170) cc_final: 0.6396 (ttm-80) REVERT: J 192 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7108 (ptm) REVERT: J 291 ILE cc_start: 0.8579 (mt) cc_final: 0.8238 (pt) REVERT: J 304 ASP cc_start: 0.6464 (m-30) cc_final: 0.6176 (m-30) REVERT: J 322 ARG cc_start: 0.7063 (ttp-110) cc_final: 0.6600 (mtm110) REVERT: J 325 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7668 (mttp) REVERT: J 545 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8327 (p90) REVERT: J 684 ASP cc_start: 0.8032 (t0) cc_final: 0.7744 (t0) REVERT: J 895 CYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6956 (p) REVERT: J 1318 SER cc_start: 0.8404 (m) cc_final: 0.7417 (t) REVERT: J 1349 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: J 1373 ARG cc_start: 0.4893 (ttp80) cc_final: 0.4549 (ttm-80) REVERT: K 11 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6900 (mt-10) REVERT: K 56 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.5909 (mp0) REVERT: L 10 LYS cc_start: 0.6473 (mmtp) cc_final: 0.5930 (ptmt) REVERT: L 35 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7087 (mt) REVERT: L 88 GLU cc_start: 0.5396 (OUTLIER) cc_final: 0.5165 (mm-30) REVERT: L 102 MET cc_start: 0.7717 (mmm) cc_final: 0.7381 (mmm) REVERT: L 113 ARG cc_start: 0.5796 (tpt90) cc_final: 0.5425 (mtm-85) REVERT: L 273 MET cc_start: 0.4615 (tpt) cc_final: 0.3647 (tpp) REVERT: L 433 TRP cc_start: 0.6665 (t60) cc_final: 0.6209 (t60) REVERT: L 436 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7593 (tpp80) REVERT: L 437 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: L 485 GLU cc_start: 0.5234 (OUTLIER) cc_final: 0.5033 (tt0) REVERT: L 491 GLU cc_start: 0.6190 (mp0) cc_final: 0.5971 (mp0) REVERT: L 561 MET cc_start: 0.8076 (mtm) cc_final: 0.7860 (mtp) outliers start: 350 outliers final: 243 residues processed: 830 average time/residue: 0.2222 time to fit residues: 289.0022 Evaluate side-chains 677 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 413 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 222 THR Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 160 ASP Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 443 ASP Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 577 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 731 ARG Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 759 SER Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 815 SER Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 948 ILE Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1003 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1226 THR Chi-restraints excluded: chain I residue 1235 LEU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1269 ARG Chi-restraints excluded: chain I residue 1301 ARG Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 325 LYS Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 384 LYS Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 486 SER Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 514 THR Chi-restraints excluded: chain J residue 515 ARG Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 611 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 655 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 720 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 884 SER Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 907 HIS Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 985 ILE Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain J residue 1268 ASN Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1328 THR Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 315 TRP Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 437 GLN Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 494 ILE Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 55 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN G 23 HIS G 147 GLN H 128 HIS H 194 GLN I 31 GLN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN I 343 HIS I 437 ASN I 573 ASN I 618 GLN I 659 GLN I 799 ASN I 808 ASN I1009 ASN I1116 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1257 GLN J 196 GLN J 276 ASN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN J 424 ASN J 450 HIS J 465 GLN J 477 GLN J 489 ASN J 680 ASN J 700 ASN J 762 ASN J 777 HIS J1108 GLN J1114 GLN J1235 ASN J1249 ASN L 227 GLN L 258 GLN L 437 GLN N 42 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.177746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144330 restraints weight = 42687.972| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.36 r_work: 0.3296 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32824 Z= 0.164 Angle : 0.711 14.135 44655 Z= 0.365 Chirality : 0.046 0.202 5125 Planarity : 0.005 0.058 5564 Dihedral : 16.863 172.692 5832 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.07 % Favored : 92.82 % Rotamer: Outliers : 7.45 % Allowed : 24.06 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.72 (0.12), residues: 3874 helix: -0.95 (0.12), residues: 1584 sheet: -2.75 (0.23), residues: 400 loop : -2.33 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 339 TYR 0.024 0.002 TYR G 177 PHE 0.021 0.002 PHE I 545 TRP 0.013 0.002 TRP I 807 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00377 (32812) covalent geometry : angle 0.69612 (44637) hydrogen bonds : bond 0.04865 ( 1406) hydrogen bonds : angle 5.29299 ( 3886) metal coordination : bond 0.02084 ( 12) metal coordination : angle 7.18541 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 498 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 HIS cc_start: 0.4508 (OUTLIER) cc_final: 0.3788 (p-80) REVERT: G 181 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6581 (mm-30) REVERT: H 206 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: I 20 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6511 (mm-40) REVERT: I 240 GLU cc_start: 0.5384 (tm-30) cc_final: 0.5162 (tp30) REVERT: I 301 TYR cc_start: 0.4609 (OUTLIER) cc_final: 0.4183 (m-10) REVERT: I 360 LEU cc_start: 0.7429 (tt) cc_final: 0.7122 (mm) REVERT: I 407 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7096 (mtp180) REVERT: I 422 LYS cc_start: 0.8021 (ptmt) cc_final: 0.7353 (mmtt) REVERT: I 478 ARG cc_start: 0.6764 (tmt-80) cc_final: 0.6361 (tpt90) REVERT: I 503 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7635 (tptt) REVERT: I 624 ASP cc_start: 0.7479 (t0) cc_final: 0.7129 (t0) REVERT: I 641 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: I 951 MET cc_start: 0.8265 (ttm) cc_final: 0.7939 (ttp) REVERT: I 964 LEU cc_start: 0.6876 (tp) cc_final: 0.6474 (tp) REVERT: I 1012 GLU cc_start: 0.4741 (tt0) cc_final: 0.4455 (mt-10) REVERT: I 1211 ARG cc_start: 0.7733 (ptp90) cc_final: 0.7471 (mtm-85) REVERT: I 1304 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8363 (ttm) REVERT: J 87 LYS cc_start: 0.6683 (tppt) cc_final: 0.6352 (ttmt) REVERT: J 170 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6530 (mm-30) REVERT: J 221 ILE cc_start: 0.7118 (mt) cc_final: 0.6911 (tt) REVERT: J 267 ASP cc_start: 0.7345 (m-30) cc_final: 0.7098 (m-30) REVERT: J 270 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7099 (mtp-110) REVERT: J 291 ILE cc_start: 0.8557 (mt) cc_final: 0.8047 (pt) REVERT: J 322 ARG cc_start: 0.6863 (ttp-110) cc_final: 0.6534 (mtm110) REVERT: J 400 MET cc_start: 0.8184 (mtp) cc_final: 0.7794 (mtp) REVERT: J 610 ARG cc_start: 0.8064 (mmt-90) cc_final: 0.7705 (ttp-170) REVERT: J 680 ASN cc_start: 0.8293 (m-40) cc_final: 0.7988 (m110) REVERT: J 684 ASP cc_start: 0.8240 (t0) cc_final: 0.7970 (t0) REVERT: J 1003 LEU cc_start: 0.4244 (OUTLIER) cc_final: 0.3794 (mp) REVERT: J 1261 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9073 (pp) REVERT: J 1373 ARG cc_start: 0.5013 (ttp80) cc_final: 0.4578 (ttm170) REVERT: K 53 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8630 (mt-10) REVERT: K 55 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: K 56 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: L 10 LYS cc_start: 0.6211 (mmtp) cc_final: 0.5719 (pttm) REVERT: L 26 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: L 35 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7105 (mt) REVERT: L 66 MET cc_start: 0.5535 (ptp) cc_final: 0.5126 (ptm) REVERT: L 105 MET cc_start: 0.6187 (ttp) cc_final: 0.5900 (ttp) REVERT: L 433 TRP cc_start: 0.7059 (t60) cc_final: 0.6491 (t60) REVERT: L 436 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7600 (tpp80) REVERT: L 521 ASP cc_start: 0.8075 (m-30) cc_final: 0.7780 (m-30) REVERT: L 551 LEU cc_start: 0.7476 (mt) cc_final: 0.7273 (mt) outliers start: 248 outliers final: 146 residues processed: 694 average time/residue: 0.2063 time to fit residues: 229.2941 Evaluate side-chains 564 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 405 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 948 ILE Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 270 ARG Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 384 LYS Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1268 ASN Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 219 GLU Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 443 ILE Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 362 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 187 optimal weight: 0.0270 chunk 372 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 380 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 223 optimal weight: 0.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS I 41 GLN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN J 196 GLN J 651 HIS J 962 ASN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146573 restraints weight = 41789.097| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.77 r_work: 0.3291 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32824 Z= 0.139 Angle : 0.644 10.913 44655 Z= 0.332 Chirality : 0.044 0.185 5125 Planarity : 0.004 0.056 5564 Dihedral : 16.087 174.697 5556 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.84 % Favored : 93.08 % Rotamer: Outliers : 6.85 % Allowed : 24.84 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.03 (0.13), residues: 3874 helix: -0.29 (0.13), residues: 1588 sheet: -2.33 (0.25), residues: 376 loop : -2.07 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J1369 TYR 0.021 0.001 TYR G 177 PHE 0.022 0.001 PHE I 545 TRP 0.011 0.001 TRP L 315 HIS 0.027 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00317 (32812) covalent geometry : angle 0.63512 (44637) hydrogen bonds : bond 0.04322 ( 1406) hydrogen bonds : angle 4.91836 ( 3886) metal coordination : bond 0.00820 ( 12) metal coordination : angle 5.19753 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 456 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 HIS cc_start: 0.3861 (OUTLIER) cc_final: 0.3434 (p-80) REVERT: G 181 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6357 (mm-30) REVERT: H 182 ARG cc_start: 0.8402 (ttt90) cc_final: 0.8146 (ttt-90) REVERT: H 206 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: I 20 GLN cc_start: 0.6741 (mm-40) cc_final: 0.6452 (mm-40) REVERT: I 66 SER cc_start: 0.7067 (OUTLIER) cc_final: 0.6791 (p) REVERT: I 70 TYR cc_start: 0.7124 (t80) cc_final: 0.6878 (t80) REVERT: I 77 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: I 301 TYR cc_start: 0.4478 (OUTLIER) cc_final: 0.3776 (m-10) REVERT: I 316 GLU cc_start: 0.8111 (pm20) cc_final: 0.7597 (mp0) REVERT: I 370 MET cc_start: 0.6960 (mmm) cc_final: 0.6739 (mmm) REVERT: I 422 LYS cc_start: 0.8018 (ptmt) cc_final: 0.7345 (mmtt) REVERT: I 478 ARG cc_start: 0.6931 (tmt-80) cc_final: 0.6449 (tpt90) REVERT: I 503 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7632 (tptt) REVERT: I 624 ASP cc_start: 0.7084 (t0) cc_final: 0.6741 (t0) REVERT: I 641 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: I 653 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9001 (ttt) REVERT: I 800 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8345 (mmt) REVERT: I 889 PRO cc_start: 0.8389 (Cg_endo) cc_final: 0.8167 (Cg_exo) REVERT: I 951 MET cc_start: 0.8195 (ttm) cc_final: 0.7883 (ttp) REVERT: I 964 LEU cc_start: 0.6737 (tp) cc_final: 0.6433 (tp) REVERT: I 1011 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6601 (mt) REVERT: I 1012 GLU cc_start: 0.5090 (tt0) cc_final: 0.4827 (mt-10) REVERT: I 1033 ARG cc_start: 0.7810 (mtp180) cc_final: 0.7455 (ttt-90) REVERT: I 1304 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8107 (tpt) REVERT: J 221 ILE cc_start: 0.7296 (mt) cc_final: 0.7067 (tt) REVERT: J 267 ASP cc_start: 0.7311 (m-30) cc_final: 0.7109 (m-30) REVERT: J 270 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6978 (mtp-110) REVERT: J 322 ARG cc_start: 0.7042 (ttp-110) cc_final: 0.6494 (ttp-110) REVERT: J 400 MET cc_start: 0.8210 (mtp) cc_final: 0.7831 (mtp) REVERT: J 560 ASN cc_start: 0.5882 (OUTLIER) cc_final: 0.4614 (p0) REVERT: J 684 ASP cc_start: 0.8217 (t0) cc_final: 0.7995 (t0) REVERT: J 890 THR cc_start: 0.8381 (m) cc_final: 0.8060 (p) REVERT: J 1048 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.4475 (ptt180) REVERT: J 1261 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8969 (pp) REVERT: K 55 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: L 10 LYS cc_start: 0.6014 (mmtp) cc_final: 0.5434 (pttm) REVERT: L 26 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: L 66 MET cc_start: 0.5331 (ptp) cc_final: 0.5003 (ptm) REVERT: L 118 ASP cc_start: 0.5864 (OUTLIER) cc_final: 0.4949 (t70) REVERT: L 144 LEU cc_start: 0.3579 (OUTLIER) cc_final: 0.2873 (mt) REVERT: L 146 GLU cc_start: 0.3206 (OUTLIER) cc_final: 0.1333 (tp30) REVERT: L 394 TYR cc_start: 0.7949 (m-80) cc_final: 0.7550 (m-80) REVERT: L 436 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7696 (tpp80) REVERT: L 491 GLU cc_start: 0.6301 (mt-10) cc_final: 0.5880 (mp0) REVERT: L 521 ASP cc_start: 0.8045 (m-30) cc_final: 0.7798 (m-30) REVERT: M 254 LEU cc_start: 0.4348 (OUTLIER) cc_final: 0.4046 (mp) outliers start: 228 outliers final: 132 residues processed: 632 average time/residue: 0.2041 time to fit residues: 208.9596 Evaluate side-chains 559 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 406 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 383 SER Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 270 ARG Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 384 LYS Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1048 ARG Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1268 ASN Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 219 GLU Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 494 ILE Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 6 ASP Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 339 optimal weight: 20.0000 chunk 349 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 224 optimal weight: 0.6980 chunk 385 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 336 optimal weight: 5.9990 chunk 343 optimal weight: 30.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I 832 HIS J 294 ASN J 651 HIS J 680 ASN J 777 HIS K 31 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.174125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140478 restraints weight = 41462.874| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.53 r_work: 0.3163 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32824 Z= 0.178 Angle : 0.659 10.653 44655 Z= 0.339 Chirality : 0.044 0.183 5125 Planarity : 0.004 0.058 5564 Dihedral : 15.826 173.781 5505 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 7.15 % Allowed : 24.54 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % 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: -1.77 (0.13), residues: 3874 helix: -0.04 (0.13), residues: 1585 sheet: -2.14 (0.25), residues: 388 loop : -1.96 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J1369 TYR 0.022 0.001 TYR G 177 PHE 0.018 0.001 PHE J1325 TRP 0.018 0.001 TRP L 433 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00418 (32812) covalent geometry : angle 0.65060 (44637) hydrogen bonds : bond 0.04346 ( 1406) hydrogen bonds : angle 4.85597 ( 3886) metal coordination : bond 0.00865 ( 12) metal coordination : angle 5.16615 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 421 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 160 HIS cc_start: 0.3963 (OUTLIER) cc_final: 0.3581 (p-80) REVERT: H 182 ARG cc_start: 0.8333 (ttt90) cc_final: 0.7999 (ttt-90) REVERT: H 206 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: H 226 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7527 (tt0) REVERT: I 20 GLN cc_start: 0.6899 (mm-40) cc_final: 0.6585 (mm-40) REVERT: I 66 SER cc_start: 0.7179 (OUTLIER) cc_final: 0.6681 (p) REVERT: I 295 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7380 (mmtt) REVERT: I 301 TYR cc_start: 0.4432 (OUTLIER) cc_final: 0.3980 (m-10) REVERT: I 316 GLU cc_start: 0.8018 (pm20) cc_final: 0.7426 (mp0) REVERT: I 370 MET cc_start: 0.7008 (mmm) cc_final: 0.6807 (mmm) REVERT: I 422 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7303 (mmtt) REVERT: I 478 ARG cc_start: 0.6610 (tmt-80) cc_final: 0.6156 (tpt90) REVERT: I 503 LYS cc_start: 0.8100 (tmtt) cc_final: 0.7857 (mmtp) REVERT: I 624 ASP cc_start: 0.7121 (t0) cc_final: 0.6792 (t0) REVERT: I 641 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: I 653 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.9048 (ttt) REVERT: I 889 PRO cc_start: 0.8308 (Cg_endo) cc_final: 0.8103 (Cg_exo) REVERT: I 930 ASP cc_start: 0.8047 (t0) cc_final: 0.7821 (t0) REVERT: I 951 MET cc_start: 0.8218 (ttm) cc_final: 0.7877 (ttp) REVERT: I 964 LEU cc_start: 0.6638 (tp) cc_final: 0.6307 (tp) REVERT: I 1012 GLU cc_start: 0.5110 (tt0) cc_final: 0.4725 (mt-10) REVERT: I 1033 ARG cc_start: 0.7868 (mtp180) cc_final: 0.7509 (ttt-90) REVERT: I 1304 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8241 (tpt) REVERT: J 221 ILE cc_start: 0.7117 (mt) cc_final: 0.6917 (tt) REVERT: J 270 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7019 (mtp-110) REVERT: J 322 ARG cc_start: 0.7058 (ttp-110) cc_final: 0.6667 (mtm110) REVERT: J 346 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7469 (mtt-85) REVERT: J 400 MET cc_start: 0.8315 (mtp) cc_final: 0.7893 (mtp) REVERT: J 560 ASN cc_start: 0.5825 (OUTLIER) cc_final: 0.4605 (p0) REVERT: J 684 ASP cc_start: 0.8262 (t0) cc_final: 0.8045 (t0) REVERT: J 890 THR cc_start: 0.8332 (m) cc_final: 0.7996 (p) REVERT: J 993 GLU cc_start: 0.3467 (OUTLIER) cc_final: 0.3012 (mp0) REVERT: J 1025 MET cc_start: 0.4284 (OUTLIER) cc_final: 0.3104 (mmt) REVERT: J 1261 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8972 (pp) REVERT: K 72 GLN cc_start: 0.7328 (mm-40) cc_final: 0.7112 (mt0) REVERT: L 10 LYS cc_start: 0.5937 (mmtp) cc_final: 0.5283 (pttm) REVERT: L 26 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: L 53 ILE cc_start: 0.4817 (OUTLIER) cc_final: 0.4508 (pp) REVERT: L 66 MET cc_start: 0.5401 (ptp) cc_final: 0.4998 (ptm) REVERT: L 100 MET cc_start: 0.7665 (mtp) cc_final: 0.7407 (mtp) REVERT: L 118 ASP cc_start: 0.6278 (OUTLIER) cc_final: 0.5328 (t0) REVERT: L 378 GLU cc_start: 0.6245 (mp0) cc_final: 0.5974 (mp0) REVERT: L 394 TYR cc_start: 0.7925 (m-80) cc_final: 0.7546 (m-80) REVERT: L 417 ASP cc_start: 0.7934 (t70) cc_final: 0.7595 (t0) REVERT: L 436 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7568 (tpp80) REVERT: L 571 TYR cc_start: 0.6256 (m-10) cc_final: 0.5932 (m-80) REVERT: M 254 LEU cc_start: 0.4372 (OUTLIER) cc_final: 0.4143 (mp) outliers start: 238 outliers final: 163 residues processed: 607 average time/residue: 0.2099 time to fit residues: 206.1678 Evaluate side-chains 576 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 395 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1054 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1235 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 270 ARG Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 346 ARG Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 384 LYS Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 993 GLU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1268 ASN Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 219 GLU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 494 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 536 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 6 ASP Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 378 optimal weight: 8.9990 chunk 305 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 216 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 249 optimal weight: 0.1980 chunk 140 optimal weight: 6.9990 chunk 219 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 357 ASN I 832 HIS ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 HIS J 680 ASN J1086 ASN J1114 GLN ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.146898 restraints weight = 41744.549| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.76 r_work: 0.3287 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32824 Z= 0.137 Angle : 0.615 11.548 44655 Z= 0.318 Chirality : 0.043 0.246 5125 Planarity : 0.004 0.060 5564 Dihedral : 15.634 176.104 5494 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 6.19 % Allowed : 25.86 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % 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: -1.52 (0.13), residues: 3874 helix: 0.22 (0.13), residues: 1599 sheet: -1.97 (0.25), residues: 388 loop : -1.89 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1369 TYR 0.020 0.001 TYR G 177 PHE 0.019 0.001 PHE I 545 TRP 0.017 0.001 TRP L 433 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00315 (32812) covalent geometry : angle 0.60923 (44637) hydrogen bonds : bond 0.04016 ( 1406) hydrogen bonds : angle 4.69789 ( 3886) metal coordination : bond 0.00671 ( 12) metal coordination : angle 4.39623 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 430 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.5984 (mp0) REVERT: G 160 HIS cc_start: 0.3909 (OUTLIER) cc_final: 0.3591 (p-80) REVERT: H 182 ARG cc_start: 0.8252 (ttt90) cc_final: 0.7963 (ttt-90) REVERT: H 206 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: I 20 GLN cc_start: 0.6840 (mm-40) cc_final: 0.6625 (mm-40) REVERT: I 187 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7476 (mm-30) REVERT: I 295 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7618 (mmtt) REVERT: I 301 TYR cc_start: 0.4556 (OUTLIER) cc_final: 0.4059 (m-10) REVERT: I 316 GLU cc_start: 0.8094 (pm20) cc_final: 0.7575 (mp0) REVERT: I 370 MET cc_start: 0.7193 (mmm) cc_final: 0.6894 (mmm) REVERT: I 403 MET cc_start: 0.8609 (tmm) cc_final: 0.7828 (tmm) REVERT: I 422 LYS cc_start: 0.8002 (ptmt) cc_final: 0.7297 (mmtt) REVERT: I 478 ARG cc_start: 0.6714 (tmt-80) cc_final: 0.6277 (tpt90) REVERT: I 624 ASP cc_start: 0.7022 (t0) cc_final: 0.6732 (t0) REVERT: I 641 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: I 653 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8977 (ttt) REVERT: I 889 PRO cc_start: 0.8300 (Cg_endo) cc_final: 0.7995 (Cg_exo) REVERT: I 1011 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6463 (mt) REVERT: I 1012 GLU cc_start: 0.5242 (tt0) cc_final: 0.4989 (mt-10) REVERT: I 1033 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7556 (ttt-90) REVERT: I 1304 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8176 (tpt) REVERT: J 193 ASP cc_start: 0.6565 (t0) cc_final: 0.6320 (t0) REVERT: J 322 ARG cc_start: 0.6755 (ttp-110) cc_final: 0.6383 (mtm110) REVERT: J 346 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7421 (mtt-85) REVERT: J 400 MET cc_start: 0.8285 (mtp) cc_final: 0.7891 (mtp) REVERT: J 560 ASN cc_start: 0.5901 (OUTLIER) cc_final: 0.4746 (p0) REVERT: J 587 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8906 (mt) REVERT: J 604 MET cc_start: 0.8599 (ttp) cc_final: 0.8316 (ttp) REVERT: J 747 MET cc_start: 0.8817 (mmm) cc_final: 0.8598 (mmp) REVERT: J 890 THR cc_start: 0.8487 (m) cc_final: 0.8086 (p) REVERT: J 993 GLU cc_start: 0.3816 (OUTLIER) cc_final: 0.3329 (mp0) REVERT: J 1025 MET cc_start: 0.4279 (OUTLIER) cc_final: 0.3268 (mmt) REVERT: J 1095 MET cc_start: 0.4390 (mtm) cc_final: 0.4133 (mtm) REVERT: J 1114 GLN cc_start: 0.5001 (OUTLIER) cc_final: 0.4672 (tp40) REVERT: J 1261 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8927 (pp) REVERT: K 53 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8621 (mt-10) REVERT: K 72 GLN cc_start: 0.7303 (mm-40) cc_final: 0.7091 (mt0) REVERT: L 10 LYS cc_start: 0.6057 (mmtp) cc_final: 0.5415 (pttm) REVERT: L 26 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: L 53 ILE cc_start: 0.4732 (OUTLIER) cc_final: 0.4350 (tp) REVERT: L 66 MET cc_start: 0.5378 (ptp) cc_final: 0.4971 (ptm) REVERT: L 100 MET cc_start: 0.7587 (mtp) cc_final: 0.7381 (mtp) REVERT: L 118 ASP cc_start: 0.5909 (m-30) cc_final: 0.5148 (t0) REVERT: L 146 GLU cc_start: 0.3150 (OUTLIER) cc_final: 0.1265 (tp30) REVERT: L 394 TYR cc_start: 0.7970 (m-80) cc_final: 0.7564 (m-80) REVERT: L 417 ASP cc_start: 0.7775 (t70) cc_final: 0.7558 (t0) REVERT: L 436 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7684 (tpp80) REVERT: L 571 TYR cc_start: 0.6110 (m-10) cc_final: 0.5887 (m-80) outliers start: 206 outliers final: 149 residues processed: 590 average time/residue: 0.2108 time to fit residues: 199.2432 Evaluate side-chains 563 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 395 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 346 ARG Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 384 LYS Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 718 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 993 GLU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1114 GLN Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1268 ASN Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 536 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 6 ASP Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 347 optimal weight: 10.0000 chunk 329 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 363 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS J 294 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.174127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141432 restraints weight = 41423.480| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.46 r_work: 0.3162 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32824 Z= 0.184 Angle : 0.651 11.835 44655 Z= 0.334 Chirality : 0.044 0.245 5125 Planarity : 0.004 0.059 5564 Dihedral : 15.649 175.141 5476 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer: Outliers : 7.27 % Allowed : 25.80 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % 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: -1.49 (0.13), residues: 3874 helix: 0.20 (0.13), residues: 1606 sheet: -1.94 (0.25), residues: 379 loop : -1.85 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J1369 TYR 0.021 0.002 TYR G 177 PHE 0.017 0.002 PHE J1325 TRP 0.015 0.001 TRP L 433 HIS 0.007 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00434 (32812) covalent geometry : angle 0.64407 (44637) hydrogen bonds : bond 0.04211 ( 1406) hydrogen bonds : angle 4.75256 ( 3886) metal coordination : bond 0.00882 ( 12) metal coordination : angle 4.75115 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 399 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 LEU cc_start: 0.7574 (mt) cc_final: 0.7314 (mt) REVERT: G 76 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: G 160 HIS cc_start: 0.3828 (OUTLIER) cc_final: 0.3536 (p-80) REVERT: G 205 MET cc_start: 0.8744 (ptp) cc_final: 0.8458 (ptm) REVERT: H 182 ARG cc_start: 0.8572 (ttt90) cc_final: 0.8236 (ttt-90) REVERT: H 206 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: H 226 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7948 (tt0) REVERT: I 20 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6749 (mm-40) REVERT: I 66 SER cc_start: 0.7279 (OUTLIER) cc_final: 0.6758 (p) REVERT: I 187 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7739 (mm-30) REVERT: I 295 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7603 (mmtt) REVERT: I 301 TYR cc_start: 0.4568 (OUTLIER) cc_final: 0.4177 (m-10) REVERT: I 316 GLU cc_start: 0.8131 (pm20) cc_final: 0.7643 (mp0) REVERT: I 378 ARG cc_start: 0.5431 (ptm160) cc_final: 0.5154 (ptm160) REVERT: I 422 LYS cc_start: 0.8062 (ptmt) cc_final: 0.7319 (mmtt) REVERT: I 472 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7749 (pp20) REVERT: I 478 ARG cc_start: 0.6789 (tmt-80) cc_final: 0.6301 (tpt90) REVERT: I 624 ASP cc_start: 0.7273 (t0) cc_final: 0.6982 (t0) REVERT: I 641 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: I 653 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9137 (ttt) REVERT: I 889 PRO cc_start: 0.8303 (Cg_endo) cc_final: 0.8010 (Cg_exo) REVERT: I 964 LEU cc_start: 0.7121 (tp) cc_final: 0.6560 (tp) REVERT: I 1012 GLU cc_start: 0.5145 (tt0) cc_final: 0.4787 (mt-10) REVERT: I 1033 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7652 (ttt-90) REVERT: I 1304 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8408 (tpt) REVERT: J 176 PHE cc_start: 0.5910 (t80) cc_final: 0.5597 (t80) REVERT: J 322 ARG cc_start: 0.6927 (ttp-110) cc_final: 0.6511 (mtm110) REVERT: J 346 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7691 (mtt-85) REVERT: J 384 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8114 (mptp) REVERT: J 560 ASN cc_start: 0.5998 (OUTLIER) cc_final: 0.4763 (p0) REVERT: J 587 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9024 (mt) REVERT: J 747 MET cc_start: 0.8910 (mmm) cc_final: 0.8695 (mmp) REVERT: J 806 ASP cc_start: 0.8690 (m-30) cc_final: 0.8474 (m-30) REVERT: J 890 THR cc_start: 0.8457 (m) cc_final: 0.8031 (p) REVERT: J 993 GLU cc_start: 0.3363 (OUTLIER) cc_final: 0.2946 (mp0) REVERT: J 1025 MET cc_start: 0.4299 (OUTLIER) cc_final: 0.3096 (mmt) REVERT: J 1261 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9044 (pp) REVERT: K 11 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7083 (mt-10) REVERT: K 41 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: L 10 LYS cc_start: 0.6004 (mmtp) cc_final: 0.5287 (pttm) REVERT: L 26 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: L 66 MET cc_start: 0.5502 (ptt) cc_final: 0.5057 (ptm) REVERT: L 118 ASP cc_start: 0.6138 (OUTLIER) cc_final: 0.5158 (t0) REVERT: L 146 GLU cc_start: 0.3514 (OUTLIER) cc_final: 0.1842 (tp30) REVERT: L 417 ASP cc_start: 0.7889 (t70) cc_final: 0.7682 (t0) REVERT: L 436 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7838 (tpp-160) REVERT: L 571 TYR cc_start: 0.6647 (m-10) cc_final: 0.6293 (m-80) outliers start: 242 outliers final: 182 residues processed: 594 average time/residue: 0.2110 time to fit residues: 201.8224 Evaluate side-chains 582 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 379 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 383 SER Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1235 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 270 ARG Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 346 ARG Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 384 LYS Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 718 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 993 GLU Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1268 ASN Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 118 ASP Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 494 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 536 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 6 ASP Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 258 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 312 optimal weight: 0.0370 chunk 322 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS I 922 ASN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1114 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142929 restraints weight = 41580.080| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.24 r_work: 0.3210 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32824 Z= 0.143 Angle : 0.612 12.935 44655 Z= 0.316 Chirality : 0.043 0.196 5125 Planarity : 0.004 0.060 5564 Dihedral : 15.545 177.362 5471 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.50 % Rotamer: Outliers : 6.64 % Allowed : 26.34 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % 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: -1.30 (0.13), residues: 3874 helix: 0.41 (0.13), residues: 1594 sheet: -1.92 (0.24), residues: 397 loop : -1.75 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I1211 TYR 0.032 0.001 TYR L 137 PHE 0.017 0.001 PHE J1325 TRP 0.015 0.001 TRP L 433 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00334 (32812) covalent geometry : angle 0.60706 (44637) hydrogen bonds : bond 0.03928 ( 1406) hydrogen bonds : angle 4.63512 ( 3886) metal coordination : bond 0.00658 ( 12) metal coordination : angle 4.09283 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 413 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: G 160 HIS cc_start: 0.3764 (OUTLIER) cc_final: 0.3556 (p-80) REVERT: G 205 MET cc_start: 0.8726 (ptp) cc_final: 0.8478 (ptm) REVERT: H 182 ARG cc_start: 0.8540 (ttt90) cc_final: 0.8246 (ttt-90) REVERT: H 206 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: H 226 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7994 (tt0) REVERT: I 20 GLN cc_start: 0.7040 (mm-40) cc_final: 0.6728 (mm-40) REVERT: I 66 SER cc_start: 0.7237 (OUTLIER) cc_final: 0.6752 (p) REVERT: I 295 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7575 (mmtt) REVERT: I 316 GLU cc_start: 0.7988 (pm20) cc_final: 0.7546 (mp0) REVERT: I 334 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.5246 (pm20) REVERT: I 378 ARG cc_start: 0.5376 (ptm160) cc_final: 0.5043 (ptm160) REVERT: I 403 MET cc_start: 0.8890 (tmm) cc_final: 0.8088 (tmm) REVERT: I 422 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7320 (mmtt) REVERT: I 472 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7696 (pp20) REVERT: I 478 ARG cc_start: 0.6696 (tmt-80) cc_final: 0.6420 (tpt90) REVERT: I 624 ASP cc_start: 0.7228 (t0) cc_final: 0.6966 (t0) REVERT: I 641 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: I 653 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9028 (ttt) REVERT: I 816 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8989 (mm) REVERT: I 889 PRO cc_start: 0.8373 (Cg_endo) cc_final: 0.8058 (Cg_exo) REVERT: I 964 LEU cc_start: 0.7136 (tp) cc_final: 0.6562 (tp) REVERT: I 1012 GLU cc_start: 0.5177 (tt0) cc_final: 0.4827 (mt-10) REVERT: I 1033 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7698 (ttt-90) REVERT: I 1216 ARG cc_start: 0.8400 (mtm180) cc_final: 0.8151 (mtm180) REVERT: I 1289 GLU cc_start: 0.8276 (pt0) cc_final: 0.8045 (pt0) REVERT: I 1304 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8322 (tpt) REVERT: J 176 PHE cc_start: 0.6131 (t80) cc_final: 0.5846 (t80) REVERT: J 221 ILE cc_start: 0.7463 (mt) cc_final: 0.7196 (tt) REVERT: J 322 ARG cc_start: 0.6872 (ttp-110) cc_final: 0.6420 (mtm110) REVERT: J 346 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7668 (mtt-85) REVERT: J 400 MET cc_start: 0.8514 (mtp) cc_final: 0.8178 (mtp) REVERT: J 560 ASN cc_start: 0.5867 (OUTLIER) cc_final: 0.4666 (p0) REVERT: J 587 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8991 (mt) REVERT: J 677 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8186 (tp30) REVERT: J 747 MET cc_start: 0.8863 (mmm) cc_final: 0.8654 (mmp) REVERT: J 806 ASP cc_start: 0.8628 (m-30) cc_final: 0.8428 (m-30) REVERT: J 890 THR cc_start: 0.8429 (m) cc_final: 0.8047 (p) REVERT: J 993 GLU cc_start: 0.3414 (OUTLIER) cc_final: 0.3118 (mp0) REVERT: J 1025 MET cc_start: 0.4407 (OUTLIER) cc_final: 0.3254 (mmt) REVERT: J 1063 ASP cc_start: 0.1157 (OUTLIER) cc_final: 0.0831 (m-30) REVERT: J 1114 GLN cc_start: 0.4698 (OUTLIER) cc_final: 0.4468 (tp40) REVERT: J 1206 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.6018 (ttt90) REVERT: J 1261 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8945 (pp) REVERT: K 11 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7178 (mt-10) REVERT: K 53 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8951 (mt-10) REVERT: L 10 LYS cc_start: 0.6103 (mmtp) cc_final: 0.5357 (pttm) REVERT: L 26 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: L 66 MET cc_start: 0.5465 (ptt) cc_final: 0.5059 (ptm) REVERT: L 95 THR cc_start: 0.6297 (m) cc_final: 0.6043 (t) REVERT: L 118 ASP cc_start: 0.5787 (m-30) cc_final: 0.5024 (t0) REVERT: L 146 GLU cc_start: 0.3340 (OUTLIER) cc_final: 0.1754 (tp30) REVERT: L 436 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7834 (tpp-160) REVERT: L 571 TYR cc_start: 0.6550 (m-10) cc_final: 0.6251 (m-80) outliers start: 221 outliers final: 169 residues processed: 592 average time/residue: 0.2143 time to fit residues: 202.8140 Evaluate side-chains 582 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 391 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 222 THR Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 334 GLU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 383 SER Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 270 ARG Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 346 ARG Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 718 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 993 GLU Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1063 ASP Chi-restraints excluded: chain J residue 1114 GLN Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1206 ARG Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 494 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 536 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 6 ASP Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 153 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 370 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 303 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS L 362 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141601 restraints weight = 41659.590| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.36 r_work: 0.3208 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32824 Z= 0.208 Angle : 0.674 13.288 44655 Z= 0.345 Chirality : 0.045 0.202 5125 Planarity : 0.004 0.060 5564 Dihedral : 15.606 175.559 5459 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.64 % Favored : 92.28 % Rotamer: Outliers : 6.64 % Allowed : 26.61 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % 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: -1.39 (0.13), residues: 3874 helix: 0.27 (0.13), residues: 1592 sheet: -1.94 (0.24), residues: 398 loop : -1.75 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I1211 TYR 0.033 0.002 TYR L 137 PHE 0.017 0.002 PHE J1325 TRP 0.014 0.001 TRP L 434 HIS 0.008 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00497 (32812) covalent geometry : angle 0.66699 (44637) hydrogen bonds : bond 0.04301 ( 1406) hydrogen bonds : angle 4.77565 ( 3886) metal coordination : bond 0.00990 ( 12) metal coordination : angle 4.88901 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 395 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: G 76 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: G 160 HIS cc_start: 0.3821 (OUTLIER) cc_final: 0.3553 (p-80) REVERT: G 205 MET cc_start: 0.8693 (ptp) cc_final: 0.8435 (ptm) REVERT: H 182 ARG cc_start: 0.8256 (ttt90) cc_final: 0.7960 (ttt-90) REVERT: H 206 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: I 66 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6730 (p) REVERT: I 295 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7421 (mmtt) REVERT: I 316 GLU cc_start: 0.8025 (pm20) cc_final: 0.7544 (mp0) REVERT: I 363 LEU cc_start: 0.7255 (mp) cc_final: 0.7041 (mp) REVERT: I 403 MET cc_start: 0.8631 (tmm) cc_final: 0.7751 (tmm) REVERT: I 422 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7296 (mmtt) REVERT: I 472 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7408 (pp20) REVERT: I 478 ARG cc_start: 0.6718 (tmt-80) cc_final: 0.6386 (tpt90) REVERT: I 624 ASP cc_start: 0.7107 (t0) cc_final: 0.6761 (t0) REVERT: I 641 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: I 653 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9103 (ttt) REVERT: I 889 PRO cc_start: 0.8370 (Cg_endo) cc_final: 0.8043 (Cg_exo) REVERT: I 1012 GLU cc_start: 0.5073 (tt0) cc_final: 0.4619 (mt-10) REVERT: I 1033 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7634 (ttt-90) REVERT: I 1304 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8291 (tpt) REVERT: J 54 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7527 (t0) REVERT: J 132 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7591 (tt) REVERT: J 221 ILE cc_start: 0.7504 (mt) cc_final: 0.7232 (tt) REVERT: J 322 ARG cc_start: 0.7062 (ttp-110) cc_final: 0.6539 (mtm110) REVERT: J 346 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7525 (mtt-85) REVERT: J 400 MET cc_start: 0.8346 (mtp) cc_final: 0.7879 (mtp) REVERT: J 560 ASN cc_start: 0.5955 (OUTLIER) cc_final: 0.4707 (p0) REVERT: J 587 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9073 (mt) REVERT: J 677 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7756 (tp30) REVERT: J 747 MET cc_start: 0.8856 (mmm) cc_final: 0.8617 (mmp) REVERT: J 806 ASP cc_start: 0.8578 (m-30) cc_final: 0.8347 (m-30) REVERT: J 890 THR cc_start: 0.8538 (m) cc_final: 0.8112 (p) REVERT: J 993 GLU cc_start: 0.3147 (OUTLIER) cc_final: 0.2775 (mp0) REVERT: J 1025 MET cc_start: 0.4207 (tpt) cc_final: 0.3053 (mmt) REVERT: J 1063 ASP cc_start: 0.0955 (OUTLIER) cc_final: 0.0691 (m-30) REVERT: J 1261 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8999 (pp) REVERT: K 11 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7181 (mt-10) REVERT: K 21 LEU cc_start: 0.8061 (mt) cc_final: 0.7764 (mt) REVERT: K 41 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: K 53 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8833 (mt-10) REVERT: L 10 LYS cc_start: 0.6001 (mmtp) cc_final: 0.5312 (pttm) REVERT: L 26 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: L 66 MET cc_start: 0.5452 (ptt) cc_final: 0.5028 (ptm) REVERT: L 118 ASP cc_start: 0.5886 (m-30) cc_final: 0.5003 (t0) REVERT: L 144 LEU cc_start: 0.4130 (OUTLIER) cc_final: 0.3282 (mt) REVERT: L 146 GLU cc_start: 0.3374 (OUTLIER) cc_final: 0.1866 (tp30) REVERT: L 436 ARG cc_start: 0.8146 (ttm170) cc_final: 0.7782 (tpp-160) REVERT: L 492 ASP cc_start: 0.6897 (t0) cc_final: 0.6611 (m-30) REVERT: L 571 TYR cc_start: 0.6675 (m-10) cc_final: 0.6360 (m-80) outliers start: 221 outliers final: 175 residues processed: 579 average time/residue: 0.2104 time to fit residues: 196.7398 Evaluate side-chains 581 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 385 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 222 THR Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 383 SER Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1235 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 270 ARG Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 346 ARG Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 384 LYS Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 718 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 993 GLU Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1063 ASP Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 494 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 536 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 6 ASP Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 258 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 392 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 336 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 127 GLN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 832 HIS ** J 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 968 ASN J1114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.173860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142100 restraints weight = 41413.907| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.04 r_work: 0.3216 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32824 Z= 0.185 Angle : 0.656 13.020 44655 Z= 0.337 Chirality : 0.044 0.194 5125 Planarity : 0.004 0.059 5564 Dihedral : 15.569 176.591 5457 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer: Outliers : 6.37 % Allowed : 26.98 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % 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: -1.38 (0.13), residues: 3874 helix: 0.28 (0.13), residues: 1598 sheet: -1.97 (0.25), residues: 388 loop : -1.75 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1211 TYR 0.031 0.002 TYR L 137 PHE 0.017 0.002 PHE J1325 TRP 0.014 0.001 TRP L 433 HIS 0.011 0.001 HIS I 673 Details of bonding type rmsd covalent geometry : bond 0.00440 (32812) covalent geometry : angle 0.64892 (44637) hydrogen bonds : bond 0.04179 ( 1406) hydrogen bonds : angle 4.74572 ( 3886) metal coordination : bond 0.00896 ( 12) metal coordination : angle 4.79304 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 388 time to evaluate : 1.191 Fit side-chains REVERT: G 13 LEU cc_start: 0.7064 (mt) cc_final: 0.6762 (mt) REVERT: G 76 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: H 182 ARG cc_start: 0.8266 (ttt90) cc_final: 0.7973 (ttt-90) REVERT: H 206 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: H 226 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7547 (tt0) REVERT: I 20 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6505 (mm-40) REVERT: I 66 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6697 (p) REVERT: I 295 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7694 (mmtt) REVERT: I 316 GLU cc_start: 0.8068 (pm20) cc_final: 0.7517 (mp0) REVERT: I 403 MET cc_start: 0.8634 (tmm) cc_final: 0.7893 (tmm) REVERT: I 422 LYS cc_start: 0.7944 (ptmt) cc_final: 0.7288 (mmtt) REVERT: I 472 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: I 478 ARG cc_start: 0.6657 (tmt-80) cc_final: 0.6362 (tpt90) REVERT: I 624 ASP cc_start: 0.7107 (t0) cc_final: 0.6759 (t0) REVERT: I 641 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: I 653 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.9068 (ttt) REVERT: I 816 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8937 (mm) REVERT: I 889 PRO cc_start: 0.8400 (Cg_endo) cc_final: 0.8089 (Cg_exo) REVERT: I 1012 GLU cc_start: 0.5267 (tt0) cc_final: 0.4831 (mt-10) REVERT: I 1033 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7647 (ttt-90) REVERT: I 1304 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8252 (tpt) REVERT: J 167 ASP cc_start: 0.7969 (m-30) cc_final: 0.7763 (m-30) REVERT: J 221 ILE cc_start: 0.7611 (mt) cc_final: 0.7320 (tt) REVERT: J 346 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7474 (mtt-85) REVERT: J 400 MET cc_start: 0.8366 (mtp) cc_final: 0.7903 (mtp) REVERT: J 560 ASN cc_start: 0.6024 (OUTLIER) cc_final: 0.4722 (p0) REVERT: J 587 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9067 (mt) REVERT: J 677 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7707 (tp30) REVERT: J 747 MET cc_start: 0.8859 (mmm) cc_final: 0.8648 (mmp) REVERT: J 806 ASP cc_start: 0.8484 (m-30) cc_final: 0.8258 (m-30) REVERT: J 822 MET cc_start: 0.7950 (mmm) cc_final: 0.7534 (mtp) REVERT: J 890 THR cc_start: 0.8499 (m) cc_final: 0.8071 (p) REVERT: J 993 GLU cc_start: 0.3697 (OUTLIER) cc_final: 0.3261 (mp0) REVERT: J 1025 MET cc_start: 0.3904 (tpt) cc_final: 0.2942 (mmt) REVERT: J 1063 ASP cc_start: 0.1150 (OUTLIER) cc_final: 0.0888 (m-30) REVERT: J 1261 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8953 (pp) REVERT: K 11 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7090 (mt-10) REVERT: K 53 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8827 (mt-10) REVERT: L 10 LYS cc_start: 0.6003 (mmtp) cc_final: 0.5506 (pttm) REVERT: L 26 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: L 35 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7020 (tt) REVERT: L 66 MET cc_start: 0.5539 (ptt) cc_final: 0.5176 (ptm) REVERT: L 118 ASP cc_start: 0.5617 (m-30) cc_final: 0.4913 (t0) REVERT: L 144 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.3512 (mt) REVERT: L 146 GLU cc_start: 0.3330 (OUTLIER) cc_final: 0.1742 (tp30) REVERT: L 417 ASP cc_start: 0.8185 (t0) cc_final: 0.7389 (m-30) REVERT: L 436 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7849 (tpp-160) REVERT: L 485 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.5227 (tm-30) REVERT: L 492 ASP cc_start: 0.7034 (t0) cc_final: 0.6716 (m-30) outliers start: 212 outliers final: 173 residues processed: 560 average time/residue: 0.2080 time to fit residues: 188.4025 Evaluate side-chains 576 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 383 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 222 THR Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 383 SER Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1235 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 270 ARG Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 346 ARG Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 683 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 718 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 993 GLU Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1063 ASP Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 494 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 536 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 6 ASP Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 46 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 355 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 374 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 229 optimal weight: 4.9990 chunk 299 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 132 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I1268 GLN ** J 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.177185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144311 restraints weight = 41796.261| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.28 r_work: 0.3287 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32824 Z= 0.122 Angle : 0.605 12.142 44655 Z= 0.313 Chirality : 0.042 0.173 5125 Planarity : 0.004 0.062 5564 Dihedral : 15.397 179.769 5456 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 5.17 % Allowed : 28.06 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % 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: -1.09 (0.13), residues: 3874 helix: 0.57 (0.13), residues: 1592 sheet: -1.83 (0.25), residues: 388 loop : -1.62 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 113 TYR 0.028 0.001 TYR L 137 PHE 0.018 0.001 PHE J1325 TRP 0.016 0.001 TRP L 433 HIS 0.005 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00275 (32812) covalent geometry : angle 0.60051 (44637) hydrogen bonds : bond 0.03738 ( 1406) hydrogen bonds : angle 4.55797 ( 3886) metal coordination : bond 0.00495 ( 12) metal coordination : angle 3.66218 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7748 Ramachandran restraints generated. 3874 Oldfield, 0 Emsley, 3874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 419 time to evaluate : 1.220 Fit side-chains REVERT: G 76 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.5994 (mp0) REVERT: G 160 HIS cc_start: 0.3976 (OUTLIER) cc_final: 0.3595 (p-80) REVERT: H 182 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7952 (ttt-90) REVERT: H 206 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: H 226 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7585 (tt0) REVERT: I 20 GLN cc_start: 0.6994 (mm-40) cc_final: 0.6522 (mm-40) REVERT: I 195 PHE cc_start: 0.8031 (m-10) cc_final: 0.7809 (m-80) REVERT: I 295 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7389 (mmtt) REVERT: I 316 GLU cc_start: 0.7909 (pm20) cc_final: 0.7314 (mp0) REVERT: I 403 MET cc_start: 0.8612 (tmm) cc_final: 0.7774 (tmm) REVERT: I 422 LYS cc_start: 0.7902 (ptmt) cc_final: 0.7226 (mmtt) REVERT: I 472 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7246 (pp20) REVERT: I 478 ARG cc_start: 0.6764 (tmt-80) cc_final: 0.6520 (tpt90) REVERT: I 624 ASP cc_start: 0.6977 (t0) cc_final: 0.6725 (t0) REVERT: I 641 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6387 (mp0) REVERT: I 653 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8951 (ttt) REVERT: I 816 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8797 (mm) REVERT: I 841 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6410 (mmm160) REVERT: I 889 PRO cc_start: 0.8282 (Cg_endo) cc_final: 0.7961 (Cg_exo) REVERT: I 1012 GLU cc_start: 0.5380 (tt0) cc_final: 0.4912 (mt-10) REVERT: I 1033 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7574 (ttt-90) REVERT: I 1106 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7608 (mtt-85) REVERT: I 1216 ARG cc_start: 0.8280 (mtm180) cc_final: 0.8028 (mtm180) REVERT: I 1304 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8149 (tpt) REVERT: J 163 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: J 176 PHE cc_start: 0.6546 (t80) cc_final: 0.6260 (t80) REVERT: J 221 ILE cc_start: 0.7542 (mt) cc_final: 0.7340 (tt) REVERT: J 267 ASP cc_start: 0.7466 (m-30) cc_final: 0.7236 (m-30) REVERT: J 322 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.6738 (ttp-110) REVERT: J 400 MET cc_start: 0.8259 (mtp) cc_final: 0.7913 (mtp) REVERT: J 560 ASN cc_start: 0.6006 (OUTLIER) cc_final: 0.4837 (p0) REVERT: J 677 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7763 (tp30) REVERT: J 731 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7754 (mtp180) REVERT: J 822 MET cc_start: 0.7622 (mmm) cc_final: 0.7284 (mtp) REVERT: J 890 THR cc_start: 0.8608 (m) cc_final: 0.8167 (p) REVERT: J 993 GLU cc_start: 0.3353 (OUTLIER) cc_final: 0.3047 (mp0) REVERT: J 1025 MET cc_start: 0.4122 (tpt) cc_final: 0.3111 (mmt) REVERT: J 1261 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8899 (pp) REVERT: K 11 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7070 (mt-10) REVERT: K 21 LEU cc_start: 0.7768 (mt) cc_final: 0.7404 (mp) REVERT: L 10 LYS cc_start: 0.6117 (mmtp) cc_final: 0.5340 (pttm) REVERT: L 26 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: L 35 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6948 (tt) REVERT: L 66 MET cc_start: 0.5387 (ptt) cc_final: 0.4971 (ptm) REVERT: L 118 ASP cc_start: 0.5713 (m-30) cc_final: 0.5068 (t0) REVERT: L 144 LEU cc_start: 0.4059 (OUTLIER) cc_final: 0.3270 (mt) REVERT: L 146 GLU cc_start: 0.3370 (OUTLIER) cc_final: 0.1796 (tp30) REVERT: L 417 ASP cc_start: 0.8269 (t0) cc_final: 0.7275 (m-30) REVERT: L 436 ARG cc_start: 0.8059 (ttm170) cc_final: 0.7680 (tpp-160) REVERT: L 492 ASP cc_start: 0.7132 (t0) cc_final: 0.6833 (m-30) REVERT: L 515 GLU cc_start: 0.5412 (mt-10) cc_final: 0.5093 (tt0) outliers start: 172 outliers final: 132 residues processed: 557 average time/residue: 0.2098 time to fit residues: 187.5306 Evaluate side-chains 544 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 393 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 361 SER Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 816 ILE Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 841 ARG Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 958 LYS Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 270 ARG Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 484 MET Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 718 SER Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 902 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 910 ASN Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 993 GLU Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1221 LEU Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 536 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 604 SER Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 72 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 48 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 234 optimal weight: 0.7980 chunk 369 optimal weight: 10.0000 chunk 331 optimal weight: 20.0000 chunk 226 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 832 HIS ** J 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.175604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.143039 restraints weight = 41569.808| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.44 r_work: 0.3257 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32824 Z= 0.153 Angle : 0.632 15.275 44655 Z= 0.324 Chirality : 0.043 0.198 5125 Planarity : 0.004 0.045 5564 Dihedral : 15.356 178.837 5445 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 5.20 % Allowed : 27.64 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.24 % 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: -1.10 (0.13), residues: 3874 helix: 0.55 (0.13), residues: 1594 sheet: -1.91 (0.25), residues: 388 loop : -1.61 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 113 TYR 0.044 0.001 TYR L 137 PHE 0.017 0.001 PHE J1325 TRP 0.014 0.001 TRP L 433 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00360 (32812) covalent geometry : angle 0.62725 (44637) hydrogen bonds : bond 0.03914 ( 1406) hydrogen bonds : angle 4.58717 ( 3886) metal coordination : bond 0.00670 ( 12) metal coordination : angle 3.98013 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8235.22 seconds wall clock time: 141 minutes 49.27 seconds (8509.27 seconds total)