Starting phenix.real_space_refine on Wed Aug 27 02:55:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5iyd_8138/08_2025/5iyd_8138.cif Found real_map, /net/cci-nas-00/data/ceres_data/5iyd_8138/08_2025/5iyd_8138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5iyd_8138/08_2025/5iyd_8138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5iyd_8138/08_2025/5iyd_8138.map" model { file = "/net/cci-nas-00/data/ceres_data/5iyd_8138/08_2025/5iyd_8138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5iyd_8138/08_2025/5iyd_8138.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 11 6.06 5 P 163 5.49 5 Mg 2 5.21 5 S 255 5.16 5 C 28936 2.51 5 N 8194 2.21 5 O 9148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46709 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 11515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1454, 11515 Classifications: {'peptide': 1454} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1384} Chain breaks: 1 Chain: "B" Number of atoms: 9317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9317 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 53, 'TRANS': 1111} Chain: "C" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2213 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1062 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1723 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "F" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 689 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1205 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "I" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1013 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 937 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2391 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 16, 'TRANS': 293} Chain: "N" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "P" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1462 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "Q" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1484 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1357 Classifications: {'peptide': 165} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 158} Chain: "S" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "T" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "X" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1645 Classifications: {'DNA': 80} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 79} Chain: "Y" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1624 Classifications: {'DNA': 80} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 79} Chain: "Z" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" 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 472 SG CYS A 71 51.734 120.671 104.038 1.00 0.00 S ATOM 776 SG CYS A 111 99.025 119.103 114.506 1.00 0.00 S ATOM 20539 SG CYS B1137 61.053 129.692 112.408 1.00 0.00 S ATOM 29208 SG CYS I 17 128.543 90.465 64.717 1.00 0.00 S Time building chain proxies: 8.86, per 1000 atoms: 0.19 Number of scatterers: 46709 At special positions: 0 Unit cell: (179.47, 217.46, 170.3, 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 11 29.99 S 255 16.00 P 163 15.00 Mg 2 11.99 O 9148 8.00 N 8194 7.00 C 28936 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 91 " 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10204 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 53 sheets defined 40.9% alpha, 19.3% beta 57 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 5.43 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.726A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.658A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.710A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.089A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 removed outlier: 4.192A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 518 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.746A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 567 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.757A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.644A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.720A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.540A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.603A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.656A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 937 through 942 removed outlier: 3.628A pdb=" N LYS A 940 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.624A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.526A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 4.817A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.549A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.601A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1180 through 1184 Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 3.666A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 removed outlier: 4.007A pdb=" N ALA A1205 " --> pdb=" O PHE A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1264 through 1268 removed outlier: 3.809A pdb=" N ASN A1267 " --> pdb=" O SER A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1295 Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.960A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.998A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.947A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.974A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1446 Processing helix chain 'A' and resid 1453 through 1461 removed outlier: 3.734A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1484 Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.859A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 4.011A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 60 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 162 through 166 removed outlier: 4.240A pdb=" N GLY B 165 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 309 Proline residue: B 303 - end of helix removed outlier: 3.520A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 332 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 378 removed outlier: 3.643A pdb=" N LYS B 361 " --> pdb=" O CYS B 357 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.629A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 435' Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.567A pdb=" N LYS B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.636A pdb=" N THR B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 636 through 646 removed outlier: 3.827A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.538A pdb=" N GLU B 671 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.506A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 732 removed outlier: 3.571A pdb=" N ASN B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 4.386A pdb=" N HIS B 741 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 844 through 848 removed outlier: 4.250A pdb=" N LYS B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.612A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.217A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1019 removed outlier: 4.011A pdb=" N LYS B1010 " --> pdb=" O VAL B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 3.972A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1107 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.539A pdb=" N ARG C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.609A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.835A pdb=" N LEU C 211 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 269 removed outlier: 3.842A pdb=" N ILE C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.561A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 52 removed outlier: 3.705A pdb=" N GLU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.638A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 121 removed outlier: 4.099A pdb=" N GLY D 120 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 2 through 25 removed outlier: 4.369A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.589A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 53 through 58 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.547A pdb=" N ALA E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.629A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 74 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.599A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.786A pdb=" N HIS J 52 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.082A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.629A pdb=" N ALA K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 52 removed outlier: 3.695A pdb=" N GLU M 51 " --> pdb=" O ASP M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 110 No H-bonds generated for 'chain 'M' and resid 108 through 110' Processing helix chain 'M' and resid 111 through 128 Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.510A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 184 Processing helix chain 'M' and resid 187 through 202 Processing helix chain 'M' and resid 211 through 222 removed outlier: 4.278A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 264 Processing helix chain 'M' and resid 270 through 279 Processing helix chain 'M' and resid 281 through 293 Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.665A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 295 through 300' Processing helix chain 'M' and resid 309 through 313 Processing helix chain 'N' and resid 10 through 33 removed outlier: 4.298A pdb=" N ASP N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE N 28 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 51 removed outlier: 3.632A pdb=" N LEU N 39 " --> pdb=" O ASP N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 318 removed outlier: 3.575A pdb=" N SER N 316 " --> pdb=" O PRO N 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 8 removed outlier: 4.060A pdb=" N TYR O 6 " --> pdb=" O TYR O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 25 Processing helix chain 'O' and resid 29 through 51 Processing helix chain 'P' and resid 153 through 157 Processing helix chain 'P' and resid 179 through 187 Processing helix chain 'P' and resid 205 through 208 Processing helix chain 'P' and resid 226 through 243 Processing helix chain 'P' and resid 269 through 277 removed outlier: 3.661A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 335 removed outlier: 3.941A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'Q' and resid 12 through 26 Processing helix chain 'Q' and resid 27 through 39 removed outlier: 4.203A pdb=" N ILE Q 36 " --> pdb=" O LEU Q 32 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Q 37 " --> pdb=" O ALA Q 33 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 53 Processing helix chain 'Q' and resid 55 through 69 Processing helix chain 'Q' and resid 102 through 119 removed outlier: 3.728A pdb=" N ASP Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 144 removed outlier: 3.561A pdb=" N ALA Q 141 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 188 Proline residue: Q 186 - end of helix Processing helix chain 'Q' and resid 188 through 202 Processing helix chain 'R' and resid 76 through 92 Processing helix chain 'R' and resid 98 through 106 Processing helix chain 'R' and resid 112 through 122 Processing helix chain 'R' and resid 122 through 127 removed outlier: 3.669A pdb=" N ASN R 127 " --> pdb=" O ALA R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 156 Processing helix chain 'R' and resid 167 through 174 removed outlier: 3.867A pdb=" N ALA R 174 " --> pdb=" O ASP R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 185 removed outlier: 4.443A pdb=" N LYS R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 223 removed outlier: 3.625A pdb=" N ARG R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 239 Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 38 through 42 Processing helix chain 'S' and resid 160 through 167 Processing helix chain 'S' and resid 173 through 180 removed outlier: 3.934A pdb=" N MET S 177 " --> pdb=" O HIS S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 15 Processing helix chain 'T' and resid 25 through 33 Processing helix chain 'T' and resid 123 through 136 removed outlier: 4.109A pdb=" N LEU T 127 " --> pdb=" O ASN T 123 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 169 Processing helix chain 'T' and resid 179 through 194 removed outlier: 3.604A pdb=" N VAL T 183 " --> pdb=" O ASP T 179 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS T 193 " --> pdb=" O SER T 189 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 207 Processing helix chain 'T' and resid 209 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.913A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 10.742A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 335 removed outlier: 3.746A pdb=" N ARG A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.686A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.792A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.395A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG H 57 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.606A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.804A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 901 through 905 Processing sheet with id=AB4, first strand: chain 'A' and resid 1309 through 1313 removed outlier: 3.541A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.245A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1320 through 1322 Processing sheet with id=AB7, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.651A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.651A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.875A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.383A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.910A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG B 255 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC6, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 552 removed outlier: 3.527A pdb=" N GLU B 551 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 576 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.972A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.972A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD2, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 4.198A pdb=" N GLN B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 794 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N TYR B 949 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N MET B 796 " --> pdb=" O TYR B 949 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 826 through 829 Processing sheet with id=AD4, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD5, first strand: chain 'B' and resid 1114 through 1119 Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 14 removed outlier: 7.246A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.775A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.634A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE2, first strand: chain 'E' and resid 147 through 150 removed outlier: 5.440A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 56 through 57 removed outlier: 3.907A pdb=" N MET F 57 " --> pdb=" O ILE F 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 84 through 93 removed outlier: 7.372A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 117 through 120 Processing sheet with id=AE6, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.522A pdb=" N ALA I 94 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'M' and resid 24 through 26 Processing sheet with id=AF1, first strand: chain 'P' and resid 291 through 295 removed outlier: 3.832A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL P 169 " --> pdb=" O GLN P 256 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET P 258 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN P 167 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY P 260 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU P 165 " --> pdb=" O GLY P 260 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR P 209 " --> pdb=" O ILE P 204 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE P 204 " --> pdb=" O THR P 209 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ALA P 190 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR O 65 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N TYR P 192 " --> pdb=" O TYR O 65 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N PHE O 67 " --> pdb=" O TYR P 192 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL O 56 " --> pdb=" O GLU O 83 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU O 83 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE O 58 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE O 81 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY O 60 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL O 79 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU O 62 " --> pdb=" O ASN O 77 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN O 77 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP O 91 " --> pdb=" O ASP O 78 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU O 80 " --> pdb=" O LYS O 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS O 89 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG O 82 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU O 87 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN N 333 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS O 94 " --> pdb=" O ASN N 333 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR N 339 " --> pdb=" O CYS O 98 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN N 333 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU N 360 " --> pdb=" O ASN N 333 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL N 335 " --> pdb=" O MET N 358 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET N 358 " --> pdb=" O VAL N 335 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS N 337 " --> pdb=" O GLY N 356 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY N 356 " --> pdb=" O CYS N 337 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR N 339 " --> pdb=" O LYS N 354 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS N 354 " --> pdb=" O TYR N 339 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER N 368 " --> pdb=" O ASP N 355 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE N 357 " --> pdb=" O ILE N 366 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE N 366 " --> pdb=" O ILE N 357 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN N 359 " --> pdb=" O ASP N 364 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP N 364 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL O 56 " --> pdb=" O PHE N 367 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS N 369 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N PHE O 58 " --> pdb=" O LYS N 369 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE N 371 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N GLY O 60 " --> pdb=" O ILE N 371 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP N 373 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU O 62 " --> pdb=" O ASP N 373 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU N 375 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR O 64 " --> pdb=" O GLU N 375 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 72 through 76 Processing sheet with id=AF3, first strand: chain 'Q' and resid 145 through 146 Processing sheet with id=AF4, first strand: chain 'R' and resid 131 through 133 removed outlier: 3.630A pdb=" N GLU R 131 " --> pdb=" O ALA R 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 165 through 166 removed outlier: 3.684A pdb=" N GLY R 165 " --> pdb=" O PHE R 202 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE R 202 " --> pdb=" O GLY R 165 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 45 through 49 removed outlier: 4.465A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ASN S 142 " --> pdb=" O LYS S 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR S 26 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR S 144 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE S 28 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE S 146 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA S 30 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ASN S 32 " --> pdb=" O PRO S 148 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N GLN T 91 " --> pdb=" O GLN T 112 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLN T 112 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU T 93 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU T 106 " --> pdb=" O THR T 97 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER T 99 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU T 104 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL T 18 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN T 112 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N GLY T 17 " --> pdb=" O GLN S 129 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN S 129 " --> pdb=" O GLY T 17 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR S 125 " --> pdb=" O VAL T 21 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL T 23 " --> pdb=" O SER S 123 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE S 135 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL S 15 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA S 137 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG S 17 " --> pdb=" O ALA S 137 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY T 41 " --> pdb=" O VAL S 16 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 45 through 49 removed outlier: 4.465A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N ASN S 142 " --> pdb=" O LYS S 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR S 26 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR S 144 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE S 28 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE S 146 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA S 30 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ASN S 32 " --> pdb=" O PRO S 148 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N GLN T 91 " --> pdb=" O GLN T 112 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLN T 112 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU T 93 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU T 106 " --> pdb=" O THR T 97 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER T 99 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU T 104 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP T 8 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY T 108 " --> pdb=" O ASP T 8 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 197 through 198 removed outlier: 3.516A pdb=" N TYR T 197 " --> pdb=" O TRP T 233 " (cutoff:3.500A) 1920 hydrogen bonds defined for protein. 5331 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 282 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 11.81 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8936 1.32 - 1.46: 16022 1.46 - 1.60: 22307 1.60 - 1.74: 241 1.74 - 1.88: 401 Bond restraints: 47907 Sorted by residual: bond pdb=" CA HIS B 939 " pdb=" C HIS B 939 " ideal model delta sigma weight residual 1.526 1.444 0.082 1.23e-02 6.61e+03 4.41e+01 bond pdb=" CA ASN A1291 " pdb=" CB ASN A1291 " ideal model delta sigma weight residual 1.528 1.631 -0.102 1.59e-02 3.96e+03 4.15e+01 bond pdb=" CA LEU A 484 " pdb=" C LEU A 484 " ideal model delta sigma weight residual 1.520 1.451 0.070 1.22e-02 6.72e+03 3.26e+01 bond pdb=" C SER A1290 " pdb=" O SER A1290 " ideal model delta sigma weight residual 1.236 1.302 -0.065 1.15e-02 7.56e+03 3.21e+01 bond pdb=" CA THR A 806 " pdb=" CB THR A 806 " ideal model delta sigma weight residual 1.532 1.444 0.087 1.57e-02 4.06e+03 3.11e+01 ... (remaining 47902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.68: 65382 14.68 - 29.36: 18 29.36 - 44.04: 1 44.04 - 58.72: 2 58.72 - 73.39: 2 Bond angle restraints: 65405 Sorted by residual: angle pdb=" C GLN C 6 " pdb=" N PRO C 7 " pdb=" CD PRO C 7 " ideal model delta sigma weight residual 125.00 51.61 73.39 4.10e+00 5.95e-02 3.20e+02 angle pdb=" N ALA I 104 " pdb=" CA ALA I 104 " pdb=" C ALA I 104 " ideal model delta sigma weight residual 112.87 92.38 20.49 1.20e+00 6.94e-01 2.92e+02 angle pdb=" N ASN C 137 " pdb=" CA ASN C 137 " pdb=" C ASN C 137 " ideal model delta sigma weight residual 110.65 89.41 21.24 1.26e+00 6.30e-01 2.84e+02 angle pdb=" N ASP M 94 " pdb=" CA ASP M 94 " pdb=" C ASP M 94 " ideal model delta sigma weight residual 114.09 90.44 23.65 1.55e+00 4.16e-01 2.33e+02 angle pdb=" C HIS I 84 " pdb=" N PRO I 85 " pdb=" CD PRO I 85 " ideal model delta sigma weight residual 125.00 65.08 59.92 4.10e+00 5.95e-02 2.14e+02 ... (remaining 65400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 27688 35.99 - 71.98: 1131 71.98 - 107.96: 82 107.96 - 143.95: 1 143.95 - 179.94: 10 Dihedral angle restraints: 28912 sinusoidal: 13150 harmonic: 15762 Sorted by residual: dihedral pdb=" CA ILE H 99 " pdb=" C ILE H 99 " pdb=" N GLU H 100 " pdb=" CA GLU H 100 " ideal model delta harmonic sigma weight residual 180.00 -85.62 -94.38 0 5.00e+00 4.00e-02 3.56e+02 dihedral pdb=" CA TYR A1308 " pdb=" C TYR A1308 " pdb=" N MET A1309 " pdb=" CA MET A1309 " ideal model delta harmonic sigma weight residual 180.00 137.37 42.63 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA ASN T 123 " pdb=" C ASN T 123 " pdb=" N TYR T 124 " pdb=" CA TYR T 124 " ideal model delta harmonic sigma weight residual 180.00 140.40 39.60 0 5.00e+00 4.00e-02 6.27e+01 ... (remaining 28909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 6998 0.165 - 0.330: 253 0.330 - 0.495: 23 0.495 - 0.660: 8 0.660 - 0.824: 2 Chirality restraints: 7284 Sorted by residual: chirality pdb=" CA THR R 224 " pdb=" N THR R 224 " pdb=" C THR R 224 " pdb=" CB THR R 224 " both_signs ideal model delta sigma weight residual False 2.53 1.70 0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" CA GLU B 77 " pdb=" N GLU B 77 " pdb=" C GLU B 77 " pdb=" CB GLU B 77 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA SER A 133 " pdb=" N SER A 133 " pdb=" C SER A 133 " pdb=" CB SER A 133 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 7281 not shown) Planarity restraints: 7920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 6 " -0.229 5.00e-02 4.00e+02 2.78e-01 1.23e+02 pdb=" N PRO C 7 " 0.459 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.211 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU P 206 " 0.162 5.00e-02 4.00e+02 2.44e-01 9.51e+01 pdb=" N PRO P 207 " -0.417 5.00e-02 4.00e+02 pdb=" CA PRO P 207 " 0.177 5.00e-02 4.00e+02 pdb=" CD PRO P 207 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 194 " -0.162 5.00e-02 4.00e+02 2.43e-01 9.47e+01 pdb=" N PRO R 195 " 0.416 5.00e-02 4.00e+02 pdb=" CA PRO R 195 " -0.177 5.00e-02 4.00e+02 pdb=" CD PRO R 195 " -0.076 5.00e-02 4.00e+02 ... (remaining 7917 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.40: 12 1.40 - 2.28: 169 2.28 - 3.15: 40121 3.15 - 4.03: 119972 4.03 - 4.90: 215848 Warning: very small nonbonded interaction distances. Nonbonded interactions: 376122 Sorted by model distance: nonbonded pdb=" C VAL Q 131 " pdb="ZN ZN Q 501 " model vdw 0.526 2.460 nonbonded pdb=" OE1 GLN B 90 " pdb=" CG LEU T 141 " model vdw 0.913 3.470 nonbonded pdb=" CA CYS I 17 " pdb="ZN ZN I 201 " model vdw 0.934 2.128 nonbonded pdb=" N ALA M 21 " pdb="ZN ZN M 401 " model vdw 1.025 2.310 nonbonded pdb=" CA VAL J 14 " pdb="ZN ZN J 101 " model vdw 1.051 2.660 ... (remaining 376117 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 47.520 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 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 : 0.014 1.646 47913 Z= 0.710 Angle : 1.732 73.394 65405 Z= 1.086 Chirality : 0.078 0.824 7284 Planarity : 0.013 0.278 7920 Dihedral : 17.387 179.937 18708 Min Nonbonded Distance : 0.526 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 3.77 % Allowed : 8.46 % Favored : 87.77 % Rotamer: Outliers : 3.28 % Allowed : 5.08 % Favored : 91.64 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.10 (0.10), residues: 5357 helix: -0.59 (0.10), residues: 1877 sheet: -0.46 (0.18), residues: 752 loop : -2.31 (0.11), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.005 ARG A 734 TYR 0.105 0.006 TYR R 236 PHE 0.087 0.004 PHE R 210 TRP 0.074 0.005 TRP R 220 HIS 0.022 0.003 HIS B 481 Details of bonding type rmsd covalent geometry : bond 0.01073 (47907) covalent geometry : angle 1.73172 (65405) hydrogen bonds : bond 0.23385 ( 2010) hydrogen bonds : angle 8.86161 ( 5613) metal coordination : bond 0.79323 ( 5) Misc. bond : bond 0.28199 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2092 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1935 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 261 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7544 (mtm110) REVERT: A 286 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7891 (mm) REVERT: A 431 PHE cc_start: 0.7476 (m-80) cc_final: 0.7135 (m-10) REVERT: A 454 ASP cc_start: 0.8202 (m-30) cc_final: 0.7804 (m-30) REVERT: A 467 MET cc_start: 0.8291 (mmt) cc_final: 0.8070 (mmm) REVERT: A 487 SER cc_start: 0.8491 (m) cc_final: 0.7655 (t) REVERT: A 535 MET cc_start: 0.8055 (ptp) cc_final: 0.7844 (ptp) REVERT: A 600 ILE cc_start: 0.9050 (mm) cc_final: 0.8708 (mm) REVERT: A 601 ASN cc_start: 0.7270 (m-40) cc_final: 0.6895 (m-40) REVERT: A 670 SER cc_start: 0.8665 (m) cc_final: 0.8420 (p) REVERT: A 769 MET cc_start: 0.8906 (mtm) cc_final: 0.8358 (mtm) REVERT: A 782 SER cc_start: 0.8664 (m) cc_final: 0.8162 (t) REVERT: A 860 ILE cc_start: 0.9278 (mt) cc_final: 0.8997 (mt) REVERT: A 868 MET cc_start: 0.7738 (mmm) cc_final: 0.7387 (mmm) REVERT: A 872 MET cc_start: 0.9046 (ptm) cc_final: 0.8808 (ptt) REVERT: A 959 MET cc_start: 0.6408 (mmt) cc_final: 0.6190 (mmt) REVERT: A 1069 LEU cc_start: 0.8505 (mt) cc_final: 0.8296 (mt) REVERT: A 1086 MET cc_start: 0.9249 (mmm) cc_final: 0.8160 (tpp) REVERT: A 1094 SER cc_start: 0.9366 (m) cc_final: 0.8918 (p) REVERT: A 1161 LEU cc_start: 0.7460 (mt) cc_final: 0.7235 (mt) REVERT: A 1412 MET cc_start: 0.8071 (ttp) cc_final: 0.7404 (ppp) REVERT: A 1415 THR cc_start: 0.8856 (p) cc_final: 0.8609 (t) REVERT: A 1424 THR cc_start: 0.8112 (p) cc_final: 0.7722 (t) REVERT: B 85 LEU cc_start: 0.7718 (tp) cc_final: 0.7496 (tp) REVERT: B 93 LEU cc_start: 0.8899 (tp) cc_final: 0.8677 (tt) REVERT: B 140 LEU cc_start: 0.5483 (OUTLIER) cc_final: 0.5063 (pp) REVERT: B 388 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7932 (m-10) REVERT: B 414 GLU cc_start: 0.6864 (tp30) cc_final: 0.6477 (tp30) REVERT: B 433 LEU cc_start: 0.8105 (mt) cc_final: 0.7874 (mp) REVERT: B 441 SER cc_start: 0.8640 (m) cc_final: 0.8210 (p) REVERT: B 525 ASN cc_start: 0.8419 (t0) cc_final: 0.8164 (t0) REVERT: B 677 MET cc_start: 0.8796 (tpp) cc_final: 0.8372 (tpp) REVERT: B 702 MET cc_start: 0.8660 (mmp) cc_final: 0.8322 (mmm) REVERT: B 728 MET cc_start: 0.8281 (mtt) cc_final: 0.7903 (mtp) REVERT: B 766 TYR cc_start: 0.7964 (m-80) cc_final: 0.6894 (m-80) REVERT: B 796 MET cc_start: 0.8352 (mtt) cc_final: 0.7975 (ttm) REVERT: B 797 ASN cc_start: 0.9144 (t0) cc_final: 0.8913 (t0) REVERT: B 905 ASP cc_start: 0.8230 (t70) cc_final: 0.8011 (t70) REVERT: B 950 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8294 (mtm-85) REVERT: B 1052 LYS cc_start: 0.8749 (tttt) cc_final: 0.8374 (tttt) REVERT: B 1121 LEU cc_start: 0.7068 (tt) cc_final: 0.6671 (mt) REVERT: B 1157 LEU cc_start: 0.9222 (tp) cc_final: 0.8816 (tp) REVERT: C 44 ILE cc_start: 0.8242 (tt) cc_final: 0.7906 (tt) REVERT: C 48 ASP cc_start: 0.8125 (t0) cc_final: 0.7604 (t0) REVERT: C 94 CYS cc_start: 0.6791 (OUTLIER) cc_final: 0.5871 (p) REVERT: E 72 MET cc_start: 0.5879 (ttp) cc_final: 0.5556 (ttp) REVERT: E 203 TYR cc_start: 0.8626 (t80) cc_final: 0.8358 (t80) REVERT: F 90 LEU cc_start: 0.9168 (tp) cc_final: 0.8818 (tt) REVERT: F 91 LEU cc_start: 0.7808 (tp) cc_final: 0.7467 (tp) REVERT: F 97 LEU cc_start: 0.8578 (tp) cc_final: 0.8303 (tp) REVERT: F 102 ILE cc_start: 0.8229 (mt) cc_final: 0.7924 (mt) REVERT: F 121 ASP cc_start: 0.6526 (p0) cc_final: 0.6296 (p0) REVERT: G 3 TYR cc_start: 0.3038 (m-80) cc_final: 0.2511 (m-80) REVERT: G 49 THR cc_start: 0.6902 (p) cc_final: 0.6463 (p) REVERT: G 90 THR cc_start: 0.5606 (p) cc_final: 0.5194 (p) REVERT: H 113 SER cc_start: 0.8226 (m) cc_final: 0.7884 (p) REVERT: I 1 MET cc_start: -0.1581 (mtt) cc_final: -0.2813 (mtt) REVERT: I 95 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7687 (p) REVERT: J 2 ILE cc_start: 0.9358 (tt) cc_final: 0.9030 (mt) REVERT: J 47 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7254 (ptt90) REVERT: J 48 MET cc_start: 0.9236 (tpp) cc_final: 0.9002 (tpp) REVERT: K 9 SER cc_start: 0.7619 (m) cc_final: 0.7153 (t) REVERT: K 21 ILE cc_start: 0.9182 (mp) cc_final: 0.8966 (mp) REVERT: K 36 ASN cc_start: 0.8272 (t0) cc_final: 0.7958 (t0) REVERT: K 91 ILE cc_start: 0.7799 (mt) cc_final: 0.7565 (mt) REVERT: M 161 SER cc_start: 0.8964 (m) cc_final: 0.8756 (t) REVERT: M 164 LEU cc_start: 0.8590 (tp) cc_final: 0.8009 (tp) REVERT: M 191 ILE cc_start: 0.8737 (mt) cc_final: 0.8430 (mt) REVERT: M 227 GLN cc_start: 0.5064 (tp40) cc_final: 0.4752 (tp40) REVERT: M 235 ILE cc_start: 0.8289 (mt) cc_final: 0.7722 (mt) REVERT: P 172 VAL cc_start: 0.3363 (p) cc_final: 0.2991 (p) REVERT: P 258 MET cc_start: 0.6959 (mtp) cc_final: 0.6568 (mtp) REVERT: P 325 PHE cc_start: 0.4599 (t80) cc_final: 0.4349 (t80) REVERT: Q 30 HIS cc_start: 0.4155 (m90) cc_final: 0.3724 (m90) REVERT: Q 168 MET cc_start: -0.0272 (mtt) cc_final: -0.1585 (mtt) REVERT: R 209 GLN cc_start: 0.1141 (OUTLIER) cc_final: 0.0146 (tt0) REVERT: T 94 THR cc_start: 0.3650 (m) cc_final: 0.2568 (m) outliers start: 157 outliers final: 32 residues processed: 2030 average time/residue: 0.2733 time to fit residues: 882.2643 Evaluate side-chains 1270 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 1229 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1407 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 209 GLN Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain S residue 166 ARG Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 153 TYR Chi-restraints excluded: chain T residue 154 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 0.6980 chunk 223 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 188 GLN A 278 HIS A 353 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN A 507 GLN A 735 GLN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 145 GLN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 838 GLN ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS C 140 ASN C 145 GLN D 43 HIS D 66 ASN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 ASN H 126 GLN H 133 HIS I 45 GLN I 67 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN K 84 GLN K 89 ASN M 98 ASN M 148 GLN ** N 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN O 27 GLN ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 ASN R 115 GLN ** S 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN S 168 ASN T 112 GLN T 131 GLN T 160 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.150133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099180 restraints weight = 103413.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099966 restraints weight = 63803.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099504 restraints weight = 49066.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100148 restraints weight = 49714.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100477 restraints weight = 42555.330| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 47913 Z= 0.219 Angle : 0.939 30.221 65405 Z= 0.489 Chirality : 0.051 0.464 7284 Planarity : 0.008 0.212 7920 Dihedral : 18.520 179.257 7799 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 1.05 % Allowed : 7.45 % Favored : 91.51 % Rotamer: Outliers : 4.89 % Allowed : 16.51 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.96 (0.11), residues: 5357 helix: 0.51 (0.11), residues: 1920 sheet: -0.28 (0.17), residues: 833 loop : -1.67 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Q 23 TYR 0.035 0.002 TYR T 212 PHE 0.049 0.003 PHE Q 180 TRP 0.038 0.003 TRP C 49 HIS 0.013 0.002 HIS N 343 Details of bonding type rmsd covalent geometry : bond 0.00490 (47907) covalent geometry : angle 0.93919 (65405) hydrogen bonds : bond 0.06139 ( 2010) hydrogen bonds : angle 5.94597 ( 5613) metal coordination : bond 0.00356 ( 5) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1652 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 1418 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.9382 (t80) cc_final: 0.9121 (t80) REVERT: A 199 TYR cc_start: 0.7394 (m-80) cc_final: 0.6940 (m-10) REVERT: A 212 LYS cc_start: 0.5647 (mttp) cc_final: 0.4916 (mmmt) REVERT: A 242 TYR cc_start: 0.8595 (m-80) cc_final: 0.8194 (m-80) REVERT: A 266 MET cc_start: 0.8374 (tmm) cc_final: 0.8091 (tmm) REVERT: A 282 ASP cc_start: 0.8902 (m-30) cc_final: 0.8649 (m-30) REVERT: A 467 MET cc_start: 0.8413 (mmt) cc_final: 0.7788 (mmm) REVERT: A 592 PHE cc_start: 0.8940 (t80) cc_final: 0.8628 (t80) REVERT: A 620 HIS cc_start: 0.8363 (m-70) cc_final: 0.8024 (m90) REVERT: A 733 LEU cc_start: 0.9224 (mm) cc_final: 0.8990 (mm) REVERT: A 742 ASN cc_start: 0.8822 (t0) cc_final: 0.8131 (m-40) REVERT: A 782 SER cc_start: 0.9197 (m) cc_final: 0.8935 (t) REVERT: A 869 GLU cc_start: 0.7894 (pt0) cc_final: 0.7583 (pt0) REVERT: A 876 ASP cc_start: 0.9080 (p0) cc_final: 0.8648 (p0) REVERT: A 964 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 1024 ASN cc_start: 0.8234 (t0) cc_final: 0.8002 (t0) REVERT: A 1071 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 1086 MET cc_start: 0.9246 (mmm) cc_final: 0.8741 (tpp) REVERT: A 1094 SER cc_start: 0.9217 (m) cc_final: 0.8862 (p) REVERT: A 1229 GLU cc_start: 0.8696 (mp0) cc_final: 0.8476 (pm20) REVERT: A 1262 MET cc_start: 0.8124 (tpp) cc_final: 0.7715 (tpt) REVERT: A 1306 LYS cc_start: 0.5703 (OUTLIER) cc_final: 0.5323 (pptt) REVERT: A 1310 HIS cc_start: 0.6983 (t-170) cc_final: 0.6739 (t70) REVERT: A 1320 ILE cc_start: 0.8862 (mm) cc_final: 0.8303 (tp) REVERT: A 1332 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7117 (tp40) REVERT: A 1404 THR cc_start: 0.8590 (m) cc_final: 0.8297 (t) REVERT: A 1412 MET cc_start: 0.8501 (ttp) cc_final: 0.7489 (ppp) REVERT: A 1451 MET cc_start: 0.7181 (mtp) cc_final: 0.6840 (mtp) REVERT: B 89 GLU cc_start: 0.7484 (tp30) cc_final: 0.7183 (tp30) REVERT: B 93 LEU cc_start: 0.9078 (tp) cc_final: 0.8758 (tt) REVERT: B 108 MET cc_start: 0.8639 (ttm) cc_final: 0.8426 (ttm) REVERT: B 250 SER cc_start: 0.3826 (OUTLIER) cc_final: 0.3119 (t) REVERT: B 262 TYR cc_start: 0.7586 (m-80) cc_final: 0.7306 (m-10) REVERT: B 302 LYS cc_start: 0.9306 (tppp) cc_final: 0.9024 (tppt) REVERT: B 304 SER cc_start: 0.8918 (m) cc_final: 0.8588 (p) REVERT: B 422 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7937 (t80) REVERT: B 438 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7966 (ttp-110) REVERT: B 441 SER cc_start: 0.8851 (m) cc_final: 0.8283 (p) REVERT: B 485 LEU cc_start: 0.9181 (pp) cc_final: 0.8963 (pt) REVERT: B 526 LEU cc_start: 0.8768 (tp) cc_final: 0.8529 (mt) REVERT: B 590 LEU cc_start: 0.9082 (mt) cc_final: 0.8687 (mt) REVERT: B 677 MET cc_start: 0.9257 (tpp) cc_final: 0.8889 (tpp) REVERT: B 743 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8046 (mtp-110) REVERT: B 766 TYR cc_start: 0.8548 (m-80) cc_final: 0.7998 (m-10) REVERT: B 791 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8291 (mm-30) REVERT: B 818 GLU cc_start: 0.8027 (tt0) cc_final: 0.7546 (tt0) REVERT: B 954 MET cc_start: 0.9051 (mmt) cc_final: 0.8777 (mmt) REVERT: B 975 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8042 (mtt90) REVERT: B 1121 LEU cc_start: 0.8291 (tt) cc_final: 0.7851 (mt) REVERT: B 1143 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8551 (tttt) REVERT: B 1172 MET cc_start: 0.8302 (mtp) cc_final: 0.7597 (mtp) REVERT: C 133 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.6274 (ptt-90) REVERT: C 260 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8304 (tm-30) REVERT: D 40 LEU cc_start: 0.9205 (mt) cc_final: 0.8913 (mt) REVERT: E 18 MET cc_start: 0.8682 (mtt) cc_final: 0.8294 (ttm) REVERT: E 47 LYS cc_start: 0.4999 (OUTLIER) cc_final: 0.4792 (mmtm) REVERT: E 72 MET cc_start: 0.7680 (ttp) cc_final: 0.7388 (ttp) REVERT: E 73 PHE cc_start: 0.8423 (t80) cc_final: 0.7758 (t80) REVERT: F 61 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8229 (mp0) REVERT: F 62 ARG cc_start: 0.7963 (ttm110) cc_final: 0.6641 (ttm110) REVERT: F 87 THR cc_start: 0.8654 (p) cc_final: 0.8445 (p) REVERT: F 97 LEU cc_start: 0.9519 (tp) cc_final: 0.9269 (tp) REVERT: G 3 TYR cc_start: 0.8577 (m-80) cc_final: 0.8098 (m-10) REVERT: G 24 ASN cc_start: 0.9124 (t0) cc_final: 0.8847 (t0) REVERT: G 41 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8392 (ptmt) REVERT: G 50 THR cc_start: 0.8993 (p) cc_final: 0.8767 (t) REVERT: G 71 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8378 (mmmt) REVERT: G 112 SER cc_start: 0.8875 (m) cc_final: 0.8629 (m) REVERT: G 141 ASP cc_start: 0.7395 (m-30) cc_final: 0.7033 (m-30) REVERT: G 164 MET cc_start: 0.9010 (mtt) cc_final: 0.8671 (mmm) REVERT: G 167 TYR cc_start: 0.8409 (m-10) cc_final: 0.8105 (m-10) REVERT: H 36 LYS cc_start: 0.7088 (pttp) cc_final: 0.5356 (tptt) REVERT: H 37 MET cc_start: 0.7187 (mmm) cc_final: 0.5707 (mpp) REVERT: H 95 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7706 (ttmm) REVERT: I 1 MET cc_start: -0.0992 (mtt) cc_final: -0.1702 (mtt) REVERT: I 54 TYR cc_start: 0.9206 (t80) cc_final: 0.8797 (t80) REVERT: J 7 CYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8763 (p) REVERT: J 12 LYS cc_start: 0.9202 (ttpt) cc_final: 0.8975 (ttpp) REVERT: J 57 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7385 (tm-30) REVERT: K 18 LYS cc_start: 0.9189 (tptt) cc_final: 0.8886 (tptm) REVERT: K 74 ARG cc_start: 0.8919 (ttm170) cc_final: 0.8713 (ttm-80) REVERT: K 97 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8166 (mm-30) REVERT: L 29 LYS cc_start: 0.7759 (ptmm) cc_final: 0.6707 (ttpp) REVERT: L 56 ASP cc_start: 0.8300 (p0) cc_final: 0.7895 (p0) REVERT: M 106 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8725 (m) REVERT: M 112 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.7141 (mmt90) REVERT: M 116 ASN cc_start: 0.8628 (m110) cc_final: 0.7763 (m110) REVERT: M 120 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7648 (mm-30) REVERT: M 144 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7716 (tt0) REVERT: M 164 LEU cc_start: 0.9445 (tp) cc_final: 0.9244 (tp) REVERT: M 165 TYR cc_start: 0.8786 (t80) cc_final: 0.8424 (t80) REVERT: M 179 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8572 (mt-10) REVERT: M 215 MET cc_start: 0.8301 (mmm) cc_final: 0.7686 (mmm) REVERT: M 219 CYS cc_start: 0.7548 (m) cc_final: 0.6752 (m) REVERT: M 227 GLN cc_start: 0.8187 (tp40) cc_final: 0.7964 (tp40) REVERT: M 229 GLN cc_start: 0.9408 (OUTLIER) cc_final: 0.8905 (tp40) REVERT: M 273 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8161 (pt0) REVERT: M 287 GLN cc_start: 0.9016 (tt0) cc_final: 0.8808 (tt0) REVERT: M 293 TYR cc_start: 0.8438 (t80) cc_final: 0.8231 (t80) REVERT: N 15 ARG cc_start: 0.9454 (mtt90) cc_final: 0.9235 (mtt180) REVERT: N 51 MET cc_start: 0.8261 (mmm) cc_final: 0.7831 (mmm) REVERT: N 339 TYR cc_start: 0.9058 (p90) cc_final: 0.8520 (p90) REVERT: N 347 ASN cc_start: 0.8910 (p0) cc_final: 0.8641 (p0) REVERT: N 348 LYS cc_start: 0.9631 (mmmt) cc_final: 0.9222 (mmmt) REVERT: N 350 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8604 (tptp) REVERT: N 352 HIS cc_start: 0.9104 (m90) cc_final: 0.8046 (m90) REVERT: N 354 LYS cc_start: 0.9610 (pttm) cc_final: 0.8944 (pttp) REVERT: N 365 TYR cc_start: 0.8419 (m-80) cc_final: 0.7658 (m-80) REVERT: O 67 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8284 (t80) REVERT: O 91 ASP cc_start: 0.8688 (p0) cc_final: 0.8404 (p0) REVERT: P 189 ASN cc_start: 0.8035 (m-40) cc_final: 0.7790 (t0) REVERT: P 192 TYR cc_start: 0.8981 (t80) cc_final: 0.8729 (t80) REVERT: P 229 GLN cc_start: 0.9612 (mt0) cc_final: 0.9102 (tp40) REVERT: P 246 PHE cc_start: 0.8401 (m-10) cc_final: 0.7918 (m-10) REVERT: P 280 PHE cc_start: 0.8948 (m-80) cc_final: 0.8659 (m-80) REVERT: P 288 PHE cc_start: 0.7988 (t80) cc_final: 0.7580 (t80) REVERT: Q 30 HIS cc_start: 0.8352 (m90) cc_final: 0.7942 (m90) REVERT: Q 168 MET cc_start: -0.1750 (mtt) cc_final: -0.2501 (mtt) REVERT: R 209 GLN cc_start: 0.4458 (OUTLIER) cc_final: 0.4080 (mm110) REVERT: R 224 THR cc_start: 0.2541 (OUTLIER) cc_final: 0.2278 (p) REVERT: S 26 TYR cc_start: 0.8566 (m-80) cc_final: 0.8304 (m-10) REVERT: S 108 ARG cc_start: 0.6990 (mmm160) cc_final: 0.6581 (mmm160) REVERT: S 110 PHE cc_start: 0.8374 (m-80) cc_final: 0.8131 (t80) REVERT: S 168 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8105 (p0) REVERT: S 177 MET cc_start: 0.8472 (mmm) cc_final: 0.7637 (ttt) REVERT: T 28 SER cc_start: 0.9152 (p) cc_final: 0.8902 (p) REVERT: T 43 LEU cc_start: 0.9489 (pp) cc_final: 0.9262 (mm) REVERT: T 56 PHE cc_start: 0.7740 (t80) cc_final: 0.6983 (t80) REVERT: T 94 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7084 (m) REVERT: T 186 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8637 (ttt) REVERT: T 191 PHE cc_start: 0.7989 (t80) cc_final: 0.7551 (t80) outliers start: 234 outliers final: 116 residues processed: 1544 average time/residue: 0.2672 time to fit residues: 669.5510 Evaluate side-chains 1312 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1178 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1407 CYS Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 975 ARG Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1161 GLU Chi-restraints excluded: chain C residue 7 PRO Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 320 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 344 ARG Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 108 ASP Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 209 GLN Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain S residue 20 LYS Chi-restraints excluded: chain S residue 36 LYS Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 168 ASN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain T residue 60 GLU Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 159 HIS Chi-restraints excluded: chain T residue 186 MET Chi-restraints excluded: chain T residue 211 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 185 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 490 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 345 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 489 optimal weight: 20.0000 chunk 113 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 735 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 722 ASN B 986 GLN B1097 HIS ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN I 46 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN M 140 ASN M 148 GLN M 221 ASN ** N 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 277 HIS ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 145 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.148977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102803 restraints weight = 102422.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098728 restraints weight = 71867.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.099800 restraints weight = 62386.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100908 restraints weight = 49284.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100995 restraints weight = 43653.218| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 47913 Z= 0.205 Angle : 0.851 24.292 65405 Z= 0.439 Chirality : 0.048 0.372 7284 Planarity : 0.007 0.198 7920 Dihedral : 18.224 177.771 7745 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.84 % Favored : 91.32 % Rotamer: Outliers : 5.23 % Allowed : 18.62 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 0.82 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.76 (0.11), residues: 5357 helix: 0.69 (0.12), residues: 1902 sheet: -0.11 (0.18), residues: 796 loop : -1.55 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 153 TYR 0.058 0.002 TYR N 14 PHE 0.038 0.002 PHE Q 180 TRP 0.056 0.003 TRP T 31 HIS 0.009 0.001 HIS N 343 Details of bonding type rmsd covalent geometry : bond 0.00461 (47907) covalent geometry : angle 0.85115 (65405) hydrogen bonds : bond 0.05217 ( 2010) hydrogen bonds : angle 5.65326 ( 5613) metal coordination : bond 0.00476 ( 5) Misc. bond : bond 0.00136 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 1246 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7558 (ttm-80) REVERT: A 190 ARG cc_start: 0.7675 (mmm160) cc_final: 0.6712 (mmm160) REVERT: A 201 GLU cc_start: 0.6775 (tp30) cc_final: 0.6506 (tp30) REVERT: A 202 TRP cc_start: 0.7260 (m-10) cc_final: 0.6500 (m-10) REVERT: A 212 LYS cc_start: 0.6033 (mttp) cc_final: 0.5306 (mmmt) REVERT: A 242 TYR cc_start: 0.8592 (m-80) cc_final: 0.8219 (m-80) REVERT: A 282 ASP cc_start: 0.8748 (m-30) cc_final: 0.8433 (t70) REVERT: A 340 LYS cc_start: 0.8736 (tttm) cc_final: 0.8497 (tttt) REVERT: A 592 PHE cc_start: 0.8904 (t80) cc_final: 0.8514 (t80) REVERT: A 648 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 733 LEU cc_start: 0.9187 (mm) cc_final: 0.8907 (mm) REVERT: A 742 ASN cc_start: 0.8838 (t0) cc_final: 0.8266 (m-40) REVERT: A 869 GLU cc_start: 0.7875 (pt0) cc_final: 0.7439 (pt0) REVERT: A 876 ASP cc_start: 0.9032 (p0) cc_final: 0.8637 (p0) REVERT: A 964 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 1086 MET cc_start: 0.9183 (mmm) cc_final: 0.8656 (tpp) REVERT: A 1094 SER cc_start: 0.9122 (m) cc_final: 0.8792 (p) REVERT: A 1139 LEU cc_start: 0.8593 (tt) cc_final: 0.8390 (tt) REVERT: A 1306 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5432 (ptmt) REVERT: A 1320 ILE cc_start: 0.8886 (mm) cc_final: 0.8501 (tp) REVERT: A 1332 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7411 (tp-100) REVERT: A 1403 ASP cc_start: 0.8221 (m-30) cc_final: 0.8010 (m-30) REVERT: A 1412 MET cc_start: 0.8471 (ttp) cc_final: 0.7600 (ppp) REVERT: A 1441 GLU cc_start: 0.7995 (tp30) cc_final: 0.7618 (tp30) REVERT: A 1476 ASP cc_start: 0.8530 (t0) cc_final: 0.7950 (t0) REVERT: B 45 ASP cc_start: 0.8231 (m-30) cc_final: 0.7750 (m-30) REVERT: B 85 LEU cc_start: 0.9166 (tp) cc_final: 0.8912 (tp) REVERT: B 89 GLU cc_start: 0.7614 (tp30) cc_final: 0.7301 (tp30) REVERT: B 176 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7160 (mp0) REVERT: B 250 SER cc_start: 0.3838 (OUTLIER) cc_final: 0.2998 (t) REVERT: B 302 LYS cc_start: 0.9289 (tppp) cc_final: 0.9030 (tppt) REVERT: B 346 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8152 (tt0) REVERT: B 363 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8545 (t80) REVERT: B 405 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8282 (ttp-110) REVERT: B 422 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8089 (t80) REVERT: B 438 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8099 (ttp-110) REVERT: B 441 SER cc_start: 0.8776 (m) cc_final: 0.8361 (p) REVERT: B 485 LEU cc_start: 0.9182 (pp) cc_final: 0.8929 (pt) REVERT: B 529 MET cc_start: 0.8794 (mmm) cc_final: 0.8506 (mmm) REVERT: B 573 TRP cc_start: 0.8581 (t60) cc_final: 0.8349 (t60) REVERT: B 633 LEU cc_start: 0.9066 (tp) cc_final: 0.8829 (tp) REVERT: B 677 MET cc_start: 0.9237 (tpp) cc_final: 0.8875 (tpp) REVERT: B 702 MET cc_start: 0.9018 (mmp) cc_final: 0.8796 (mmt) REVERT: B 737 ILE cc_start: 0.8823 (pp) cc_final: 0.8414 (pp) REVERT: B 766 TYR cc_start: 0.8508 (m-80) cc_final: 0.8110 (m-10) REVERT: B 791 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8393 (mm-30) REVERT: B 818 GLU cc_start: 0.7907 (tt0) cc_final: 0.7218 (tt0) REVERT: B 954 MET cc_start: 0.9162 (mmt) cc_final: 0.8862 (mmt) REVERT: B 1121 LEU cc_start: 0.8376 (tt) cc_final: 0.7906 (mt) REVERT: B 1127 ILE cc_start: 0.7260 (pp) cc_final: 0.7022 (pp) REVERT: C 59 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8415 (mp) REVERT: C 133 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6431 (ptt-90) REVERT: C 260 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8252 (tm-30) REVERT: D 39 MET cc_start: 0.8953 (tmm) cc_final: 0.8651 (tmm) REVERT: D 40 LEU cc_start: 0.9049 (mt) cc_final: 0.8800 (mt) REVERT: D 44 ARG cc_start: 0.9088 (tpp-160) cc_final: 0.8854 (tpt-90) REVERT: D 112 LYS cc_start: 0.7630 (mmtt) cc_final: 0.7192 (mmtt) REVERT: E 31 ASP cc_start: 0.9002 (p0) cc_final: 0.8660 (p0) REVERT: E 34 ASP cc_start: 0.8705 (m-30) cc_final: 0.8431 (p0) REVERT: E 62 VAL cc_start: 0.7966 (p) cc_final: 0.6895 (p) REVERT: E 72 MET cc_start: 0.7825 (ttp) cc_final: 0.7033 (ptm) REVERT: E 73 PHE cc_start: 0.8188 (t80) cc_final: 0.7425 (t80) REVERT: E 108 GLN cc_start: 0.7956 (tp40) cc_final: 0.7747 (tp-100) REVERT: F 98 LYS cc_start: 0.9132 (tppp) cc_final: 0.8801 (tppp) REVERT: G 3 TYR cc_start: 0.8347 (m-80) cc_final: 0.8140 (m-80) REVERT: G 21 ASN cc_start: 0.8227 (p0) cc_final: 0.7874 (p0) REVERT: G 24 ASN cc_start: 0.9045 (t0) cc_final: 0.8728 (t0) REVERT: G 33 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8134 (tm-30) REVERT: G 42 TYR cc_start: 0.8940 (m-80) cc_final: 0.8310 (m-10) REVERT: G 50 THR cc_start: 0.8964 (p) cc_final: 0.8741 (t) REVERT: G 53 ASN cc_start: 0.7940 (p0) cc_final: 0.7699 (p0) REVERT: G 71 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8319 (mmmt) REVERT: G 100 GLU cc_start: 0.8797 (tp30) cc_final: 0.8357 (tp30) REVERT: G 129 LYS cc_start: 0.9456 (pptt) cc_final: 0.9212 (pptt) REVERT: G 167 TYR cc_start: 0.8067 (m-10) cc_final: 0.7801 (m-10) REVERT: H 21 LYS cc_start: 0.8351 (ptmm) cc_final: 0.7892 (tmtt) REVERT: H 35 PHE cc_start: 0.8827 (m-10) cc_final: 0.8507 (m-10) REVERT: H 36 LYS cc_start: 0.6983 (pttp) cc_final: 0.6641 (pttm) REVERT: H 56 PHE cc_start: 0.7030 (m-10) cc_final: 0.6602 (m-10) REVERT: H 95 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7686 (ttmm) REVERT: I 54 TYR cc_start: 0.9217 (t80) cc_final: 0.8755 (t80) REVERT: I 82 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8041 (tp30) REVERT: J 12 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8940 (ttpp) REVERT: J 31 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7625 (mm-30) REVERT: K 110 LYS cc_start: 0.8596 (tptp) cc_final: 0.8251 (tptp) REVERT: L 32 ASP cc_start: 0.8945 (p0) cc_final: 0.8714 (p0) REVERT: L 44 MET cc_start: 0.8365 (mmt) cc_final: 0.8101 (mmp) REVERT: M 31 ASP cc_start: 0.8844 (m-30) cc_final: 0.8520 (m-30) REVERT: M 52 TRP cc_start: 0.4062 (t60) cc_final: 0.3351 (t60) REVERT: M 82 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8521 (t) REVERT: M 112 ARG cc_start: 0.7934 (tpp-160) cc_final: 0.7377 (mtt90) REVERT: M 116 ASN cc_start: 0.8686 (m110) cc_final: 0.7588 (m-40) REVERT: M 165 TYR cc_start: 0.8815 (t80) cc_final: 0.8191 (t80) REVERT: M 181 CYS cc_start: 0.8855 (t) cc_final: 0.8600 (t) REVERT: M 229 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.9022 (tm-30) REVERT: M 287 GLN cc_start: 0.9000 (tt0) cc_final: 0.8768 (tt0) REVERT: M 300 PHE cc_start: 0.7869 (m-80) cc_final: 0.7408 (t80) REVERT: N 38 VAL cc_start: 0.7035 (p) cc_final: 0.5914 (m) REVERT: N 41 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: N 46 TRP cc_start: 0.8041 (OUTLIER) cc_final: 0.7622 (m100) REVERT: N 51 MET cc_start: 0.8191 (mmm) cc_final: 0.7627 (mmm) REVERT: N 314 LEU cc_start: 0.8453 (mm) cc_final: 0.8212 (mm) REVERT: N 344 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7752 (tmm160) REVERT: N 348 LYS cc_start: 0.9469 (mmmt) cc_final: 0.8820 (mmmt) REVERT: N 350 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8215 (tppt) REVERT: O 67 PHE cc_start: 0.8505 (t80) cc_final: 0.8099 (t80) REVERT: P 280 PHE cc_start: 0.8810 (m-80) cc_final: 0.8185 (m-80) REVERT: P 283 TYR cc_start: 0.7196 (t80) cc_final: 0.6927 (t80) REVERT: P 288 PHE cc_start: 0.7652 (t80) cc_final: 0.7353 (t80) REVERT: Q 25 PHE cc_start: 0.8397 (t80) cc_final: 0.7955 (t80) REVERT: Q 76 MET cc_start: 0.7386 (mmp) cc_final: 0.5615 (tpt) REVERT: Q 96 TYR cc_start: 0.8157 (m-80) cc_final: 0.7916 (m-80) REVERT: Q 111 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8690 (tmm160) REVERT: R 209 GLN cc_start: 0.3805 (OUTLIER) cc_final: 0.3431 (tt0) REVERT: S 14 TYR cc_start: 0.8837 (m-80) cc_final: 0.8481 (m-80) REVERT: S 17 ARG cc_start: 0.7933 (tmm-80) cc_final: 0.7495 (ttp80) REVERT: S 20 LYS cc_start: 0.8825 (tppt) cc_final: 0.8619 (tppt) REVERT: S 96 GLN cc_start: 0.7939 (mp10) cc_final: 0.7568 (mp10) REVERT: S 109 LYS cc_start: 0.7485 (mmtt) cc_final: 0.7257 (mmtt) REVERT: S 136 GLU cc_start: 0.7562 (tp30) cc_final: 0.5764 (tp30) REVERT: S 168 ASN cc_start: 0.9000 (p0) cc_final: 0.8413 (p0) REVERT: S 169 LYS cc_start: 0.7451 (ttpp) cc_final: 0.7051 (tptp) REVERT: S 177 MET cc_start: 0.8295 (mmm) cc_final: 0.7488 (ttt) REVERT: T 19 TRP cc_start: 0.7715 (m-90) cc_final: 0.7216 (m-90) REVERT: T 43 LEU cc_start: 0.9222 (pp) cc_final: 0.8983 (mm) REVERT: T 186 MET cc_start: 0.8775 (ttt) cc_final: 0.8562 (ttt) REVERT: T 191 PHE cc_start: 0.7964 (t80) cc_final: 0.7541 (t80) REVERT: T 212 TYR cc_start: 0.8639 (t80) cc_final: 0.8369 (t80) outliers start: 250 outliers final: 149 residues processed: 1402 average time/residue: 0.2570 time to fit residues: 588.0110 Evaluate side-chains 1251 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1085 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1407 CYS Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1161 GLU Chi-restraints excluded: chain C residue 7 PRO Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 340 ASP Chi-restraints excluded: chain N residue 344 ARG Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain O residue 40 PHE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 60 ARG Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 111 ARG Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 209 GLN Chi-restraints excluded: chain S residue 36 LYS Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 145 ASN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain T residue 151 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 473 optimal weight: 6.9990 chunk 347 optimal weight: 3.9990 chunk 393 optimal weight: 0.8980 chunk 328 optimal weight: 0.7980 chunk 329 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 287 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 678 ASN A 950 ASN A1005 HIS ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 42 GLN ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 716 HIS C 5 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 ASN ** N 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 GLN ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 278 GLN ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.149217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.102460 restraints weight = 102305.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098999 restraints weight = 69714.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100022 restraints weight = 58880.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101106 restraints weight = 47572.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101148 restraints weight = 42324.499| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 47913 Z= 0.190 Angle : 0.816 21.401 65405 Z= 0.420 Chirality : 0.047 0.369 7284 Planarity : 0.007 0.185 7920 Dihedral : 18.068 177.720 7734 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.32 % Favored : 91.90 % Rotamer: Outliers : 5.50 % Allowed : 19.61 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 1.23 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.69 (0.11), residues: 5357 helix: 0.71 (0.12), residues: 1893 sheet: -0.10 (0.18), residues: 757 loop : -1.43 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 138 TYR 0.033 0.002 TYR B 752 PHE 0.030 0.002 PHE Q 180 TRP 0.068 0.003 TRP T 31 HIS 0.010 0.001 HIS A1005 Details of bonding type rmsd covalent geometry : bond 0.00420 (47907) covalent geometry : angle 0.81590 (65405) hydrogen bonds : bond 0.04832 ( 2010) hydrogen bonds : angle 5.44809 ( 5613) metal coordination : bond 0.00425 ( 5) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 1177 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7722 (ttm-80) REVERT: A 199 TYR cc_start: 0.7578 (m-10) cc_final: 0.6990 (m-10) REVERT: A 233 CYS cc_start: 0.8654 (m) cc_final: 0.8363 (t) REVERT: A 242 TYR cc_start: 0.8647 (m-80) cc_final: 0.8140 (m-80) REVERT: A 266 MET cc_start: 0.7680 (tmm) cc_final: 0.7358 (tpp) REVERT: A 305 GLU cc_start: 0.8586 (tp30) cc_final: 0.8273 (tp30) REVERT: A 592 PHE cc_start: 0.8862 (t80) cc_final: 0.8505 (t80) REVERT: A 733 LEU cc_start: 0.9220 (mm) cc_final: 0.8873 (mm) REVERT: A 742 ASN cc_start: 0.8737 (t0) cc_final: 0.8091 (m-40) REVERT: A 869 GLU cc_start: 0.7703 (pt0) cc_final: 0.7383 (pt0) REVERT: A 876 ASP cc_start: 0.9076 (p0) cc_final: 0.8772 (p0) REVERT: A 964 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7846 (tm-30) REVERT: A 1004 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 1086 MET cc_start: 0.9186 (mmm) cc_final: 0.8637 (tpp) REVERT: A 1094 SER cc_start: 0.9010 (m) cc_final: 0.8729 (p) REVERT: A 1167 ARG cc_start: 0.8954 (tpt170) cc_final: 0.8743 (tpt170) REVERT: A 1212 LEU cc_start: 0.9143 (tp) cc_final: 0.8837 (mt) REVERT: A 1262 MET cc_start: 0.7143 (tpp) cc_final: 0.5952 (tpp) REVERT: A 1279 MET cc_start: 0.4341 (ppp) cc_final: 0.4040 (ppp) REVERT: A 1306 LYS cc_start: 0.5801 (OUTLIER) cc_final: 0.5204 (ptmt) REVERT: A 1320 ILE cc_start: 0.8949 (mm) cc_final: 0.8546 (tp) REVERT: A 1332 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7485 (tp-100) REVERT: A 1412 MET cc_start: 0.8591 (ttp) cc_final: 0.7694 (ppp) REVERT: A 1441 GLU cc_start: 0.7976 (tp30) cc_final: 0.7677 (tp30) REVERT: A 1476 ASP cc_start: 0.8335 (t0) cc_final: 0.8044 (t0) REVERT: A 1479 LYS cc_start: 0.8309 (mmtm) cc_final: 0.7886 (mmtm) REVERT: B 45 ASP cc_start: 0.8272 (m-30) cc_final: 0.7924 (m-30) REVERT: B 66 ASP cc_start: 0.7376 (t0) cc_final: 0.7089 (t0) REVERT: B 85 LEU cc_start: 0.9152 (tp) cc_final: 0.8932 (tp) REVERT: B 176 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7314 (mp0) REVERT: B 250 SER cc_start: 0.3861 (OUTLIER) cc_final: 0.3316 (t) REVERT: B 324 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7724 (mmm160) REVERT: B 363 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8578 (t80) REVERT: B 405 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8304 (ttp-110) REVERT: B 422 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7988 (t80) REVERT: B 438 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8096 (ttp-110) REVERT: B 441 SER cc_start: 0.8653 (m) cc_final: 0.8228 (p) REVERT: B 485 LEU cc_start: 0.9127 (pp) cc_final: 0.8862 (pt) REVERT: B 633 LEU cc_start: 0.9036 (tp) cc_final: 0.8827 (tp) REVERT: B 766 TYR cc_start: 0.8562 (m-80) cc_final: 0.8152 (m-10) REVERT: B 791 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8310 (mm-30) REVERT: B 818 GLU cc_start: 0.7742 (tt0) cc_final: 0.7088 (tt0) REVERT: B 954 MET cc_start: 0.9185 (mmt) cc_final: 0.8919 (mmt) REVERT: B 1121 LEU cc_start: 0.8255 (tt) cc_final: 0.7906 (mt) REVERT: C 6 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8593 (mm-40) REVERT: C 59 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8241 (mp) REVERT: C 158 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6877 (tm-30) REVERT: C 260 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8349 (tm-30) REVERT: D 39 MET cc_start: 0.8956 (tmm) cc_final: 0.8548 (tmm) REVERT: D 40 LEU cc_start: 0.9031 (mt) cc_final: 0.8746 (mt) REVERT: D 44 ARG cc_start: 0.9061 (tpp-160) cc_final: 0.8821 (tpt-90) REVERT: D 63 LYS cc_start: 0.9455 (ptpp) cc_final: 0.9058 (ptpp) REVERT: D 70 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7666 (ttt180) REVERT: D 112 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7593 (mmtt) REVERT: E 18 MET cc_start: 0.8696 (mtt) cc_final: 0.8375 (mtp) REVERT: E 31 ASP cc_start: 0.9026 (p0) cc_final: 0.8722 (p0) REVERT: E 34 ASP cc_start: 0.8817 (m-30) cc_final: 0.8551 (p0) REVERT: E 72 MET cc_start: 0.7787 (ttp) cc_final: 0.7317 (ttp) REVERT: E 73 PHE cc_start: 0.8086 (t80) cc_final: 0.7470 (t80) REVERT: E 108 GLN cc_start: 0.7980 (tp40) cc_final: 0.7649 (tp-100) REVERT: F 60 TYR cc_start: 0.8690 (m-80) cc_final: 0.8457 (m-80) REVERT: F 61 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8240 (mt-10) REVERT: F 95 LYS cc_start: 0.9195 (tppt) cc_final: 0.8936 (tppp) REVERT: F 121 ASP cc_start: 0.8276 (p0) cc_final: 0.7939 (p0) REVERT: G 21 ASN cc_start: 0.8136 (p0) cc_final: 0.7814 (p0) REVERT: G 24 ASN cc_start: 0.9100 (t0) cc_final: 0.8707 (t0) REVERT: G 33 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8319 (tm-30) REVERT: G 42 TYR cc_start: 0.8982 (m-80) cc_final: 0.8391 (m-10) REVERT: G 71 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8545 (mtmm) REVERT: G 73 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8837 (tppt) REVERT: G 100 GLU cc_start: 0.9003 (tp30) cc_final: 0.8631 (tp30) REVERT: G 110 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6532 (tpt90) REVERT: G 117 MET cc_start: 0.6179 (tpp) cc_final: 0.5923 (tpp) REVERT: G 167 TYR cc_start: 0.8134 (m-10) cc_final: 0.7903 (m-10) REVERT: H 21 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8113 (tmtt) REVERT: H 29 HIS cc_start: 0.8115 (m170) cc_final: 0.7825 (m170) REVERT: H 56 PHE cc_start: 0.6718 (m-10) cc_final: 0.6393 (m-10) REVERT: H 95 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7614 (ttmm) REVERT: H 99 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8378 (mt) REVERT: I 30 LYS cc_start: 0.9216 (mmtm) cc_final: 0.8892 (mmtm) REVERT: I 40 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7236 (tpp-160) REVERT: I 41 ASN cc_start: 0.8186 (p0) cc_final: 0.7415 (p0) REVERT: I 54 TYR cc_start: 0.9226 (t80) cc_final: 0.8757 (t80) REVERT: I 61 GLU cc_start: 0.7078 (pm20) cc_final: 0.6803 (pm20) REVERT: I 82 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8055 (tp30) REVERT: I 95 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7701 (m) REVERT: J 12 LYS cc_start: 0.9175 (ttpt) cc_final: 0.8971 (ttmm) REVERT: J 48 MET cc_start: 0.9075 (tpp) cc_final: 0.8479 (tpp) REVERT: J 62 TYR cc_start: 0.8497 (m-80) cc_final: 0.7956 (m-80) REVERT: K 36 ASN cc_start: 0.8849 (t0) cc_final: 0.8427 (t0) REVERT: K 49 GLN cc_start: 0.9134 (tp40) cc_final: 0.8821 (tp40) REVERT: K 93 ASP cc_start: 0.7811 (t0) cc_final: 0.7557 (t0) REVERT: K 110 LYS cc_start: 0.8598 (tptp) cc_final: 0.8234 (tptp) REVERT: L 15 MET cc_start: 0.7107 (ptt) cc_final: 0.6323 (ptt) REVERT: L 29 LYS cc_start: 0.7747 (ptmm) cc_final: 0.7188 (ttmt) REVERT: M 46 ILE cc_start: 0.3158 (OUTLIER) cc_final: 0.2539 (pp) REVERT: M 112 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.7311 (mtt90) REVERT: M 116 ASN cc_start: 0.8532 (m110) cc_final: 0.7593 (m-40) REVERT: M 120 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7327 (mm-30) REVERT: M 152 LYS cc_start: 0.7580 (tptt) cc_final: 0.7361 (tptt) REVERT: M 165 TYR cc_start: 0.8848 (t80) cc_final: 0.8495 (t80) REVERT: M 181 CYS cc_start: 0.8842 (t) cc_final: 0.8612 (t) REVERT: M 230 MET cc_start: 0.8274 (mtp) cc_final: 0.7925 (ptp) REVERT: M 300 PHE cc_start: 0.7968 (m-80) cc_final: 0.7504 (t80) REVERT: N 38 VAL cc_start: 0.7116 (p) cc_final: 0.6129 (m) REVERT: N 41 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: N 51 MET cc_start: 0.8137 (mmm) cc_final: 0.7709 (mmm) REVERT: N 312 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5469 (mm-30) REVERT: N 314 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8335 (mm) REVERT: N 339 TYR cc_start: 0.8651 (p90) cc_final: 0.8223 (p90) REVERT: N 344 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7980 (tmm160) REVERT: N 348 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9133 (mmmt) REVERT: N 349 TRP cc_start: 0.8113 (m-90) cc_final: 0.7826 (m-90) REVERT: N 350 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8497 (tppt) REVERT: O 67 PHE cc_start: 0.8704 (t80) cc_final: 0.8159 (t80) REVERT: P 189 ASN cc_start: 0.7077 (t0) cc_final: 0.6351 (t0) REVERT: P 278 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: P 280 PHE cc_start: 0.8790 (m-80) cc_final: 0.8570 (m-80) REVERT: Q 60 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8819 (ttp80) REVERT: Q 76 MET cc_start: 0.7416 (mmp) cc_final: 0.5739 (tpt) REVERT: Q 138 ASP cc_start: 0.6062 (t0) cc_final: 0.5837 (t70) REVERT: R 120 MET cc_start: 0.7499 (mmm) cc_final: 0.7294 (mmm) REVERT: R 228 MET cc_start: 0.7617 (mmm) cc_final: 0.6870 (tpp) REVERT: S 14 TYR cc_start: 0.8971 (m-80) cc_final: 0.8636 (m-80) REVERT: S 26 TYR cc_start: 0.8587 (m-80) cc_final: 0.8356 (m-80) REVERT: S 39 PHE cc_start: 0.8244 (m-10) cc_final: 0.7857 (m-10) REVERT: S 146 PHE cc_start: 0.7873 (m-10) cc_final: 0.7653 (m-10) REVERT: S 177 MET cc_start: 0.8146 (mmm) cc_final: 0.7162 (ttt) REVERT: T 124 TYR cc_start: 0.8328 (t80) cc_final: 0.8039 (t80) REVERT: T 186 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8527 (ttt) outliers start: 263 outliers final: 170 residues processed: 1327 average time/residue: 0.2423 time to fit residues: 526.6269 Evaluate side-chains 1274 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1082 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1391 SER Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1161 GLU Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 7 PRO Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 110 ARG Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 312 GLU Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 344 ARG Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 40 PHE Chi-restraints excluded: chain O residue 63 ASN Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 166 GLN Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 278 GLN Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 60 ARG Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 71 PHE Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 168 ASN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 186 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 228 optimal weight: 0.0670 chunk 361 optimal weight: 8.9990 chunk 350 optimal weight: 3.9990 chunk 519 optimal weight: 10.0000 chunk 533 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 410 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 387 optimal weight: 0.6980 chunk 341 optimal weight: 20.0000 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 606 HIS ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 145 GLN B 175 ASN B 838 GLN C 5 ASN C 25 ASN C 66 HIS D 76 ASN D 135 GLN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN I 46 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN M 148 GLN M 221 ASN M 287 GLN P 166 GLN ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.148133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100107 restraints weight = 102736.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097856 restraints weight = 69981.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098344 restraints weight = 59341.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099177 restraints weight = 49077.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099354 restraints weight = 44410.258| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 47913 Z= 0.213 Angle : 0.810 15.844 65405 Z= 0.418 Chirality : 0.047 0.382 7284 Planarity : 0.007 0.172 7920 Dihedral : 17.977 177.678 7726 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.82 % Favored : 91.45 % Rotamer: Outliers : 5.69 % Allowed : 20.44 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 0.82 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.75 (0.11), residues: 5357 helix: 0.68 (0.12), residues: 1901 sheet: -0.11 (0.19), residues: 754 loop : -1.50 (0.12), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 108 TYR 0.037 0.002 TYR B 752 PHE 0.040 0.002 PHE S 146 TRP 0.078 0.003 TRP T 31 HIS 0.010 0.001 HIS P 277 Details of bonding type rmsd covalent geometry : bond 0.00484 (47907) covalent geometry : angle 0.81020 (65405) hydrogen bonds : bond 0.04795 ( 2010) hydrogen bonds : angle 5.37360 ( 5613) metal coordination : bond 0.00307 ( 5) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 1111 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7727 (ttm-80) REVERT: A 199 TYR cc_start: 0.7618 (m-10) cc_final: 0.6906 (m-10) REVERT: A 212 LYS cc_start: 0.5633 (mmtp) cc_final: 0.4713 (mmmt) REVERT: A 233 CYS cc_start: 0.9029 (m) cc_final: 0.8492 (t) REVERT: A 242 TYR cc_start: 0.8667 (m-80) cc_final: 0.8142 (m-80) REVERT: A 266 MET cc_start: 0.7743 (tmm) cc_final: 0.7358 (tpp) REVERT: A 305 GLU cc_start: 0.8568 (tp30) cc_final: 0.8325 (tp30) REVERT: A 592 PHE cc_start: 0.8941 (t80) cc_final: 0.8663 (t80) REVERT: A 683 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7161 (tp30) REVERT: A 733 LEU cc_start: 0.9224 (mm) cc_final: 0.8888 (mm) REVERT: A 742 ASN cc_start: 0.8747 (t0) cc_final: 0.8107 (m-40) REVERT: A 869 GLU cc_start: 0.7850 (pt0) cc_final: 0.7272 (pt0) REVERT: A 876 ASP cc_start: 0.9116 (p0) cc_final: 0.8833 (p0) REVERT: A 955 GLU cc_start: 0.8857 (tp30) cc_final: 0.8390 (tp30) REVERT: A 964 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 1004 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 1086 MET cc_start: 0.9226 (mmm) cc_final: 0.8783 (tpp) REVERT: A 1094 SER cc_start: 0.9054 (m) cc_final: 0.8724 (p) REVERT: A 1167 ARG cc_start: 0.8971 (tpt170) cc_final: 0.8733 (tpt170) REVERT: A 1212 LEU cc_start: 0.9182 (tp) cc_final: 0.8868 (mt) REVERT: A 1259 ILE cc_start: 0.9521 (mm) cc_final: 0.9301 (mm) REVERT: A 1262 MET cc_start: 0.7278 (tpp) cc_final: 0.6594 (tpp) REVERT: A 1306 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5372 (ptmt) REVERT: A 1320 ILE cc_start: 0.8958 (mm) cc_final: 0.8538 (tp) REVERT: A 1332 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7507 (tp-100) REVERT: A 1412 MET cc_start: 0.8575 (ttp) cc_final: 0.7717 (ppp) REVERT: A 1441 GLU cc_start: 0.7985 (tp30) cc_final: 0.7779 (tp30) REVERT: A 1463 LEU cc_start: 0.8229 (tp) cc_final: 0.7938 (mp) REVERT: A 1476 ASP cc_start: 0.8418 (t0) cc_final: 0.8195 (t0) REVERT: B 45 ASP cc_start: 0.8296 (m-30) cc_final: 0.7976 (m-30) REVERT: B 66 ASP cc_start: 0.7461 (t0) cc_final: 0.7091 (t0) REVERT: B 85 LEU cc_start: 0.9173 (tp) cc_final: 0.8944 (tp) REVERT: B 89 GLU cc_start: 0.7691 (tp30) cc_final: 0.7253 (tp30) REVERT: B 100 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7752 (mt-10) REVERT: B 144 HIS cc_start: 0.6092 (OUTLIER) cc_final: 0.5675 (p-80) REVERT: B 250 SER cc_start: 0.4289 (OUTLIER) cc_final: 0.3710 (t) REVERT: B 255 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7549 (mmp80) REVERT: B 324 ARG cc_start: 0.8370 (mmm160) cc_final: 0.7805 (mmm160) REVERT: B 363 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8724 (t80) REVERT: B 388 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8241 (m-10) REVERT: B 422 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.8003 (t80) REVERT: B 441 SER cc_start: 0.8678 (m) cc_final: 0.8244 (p) REVERT: B 677 MET cc_start: 0.9283 (tpp) cc_final: 0.8795 (tpp) REVERT: B 733 MET cc_start: 0.7894 (ptm) cc_final: 0.7648 (ptm) REVERT: B 737 ILE cc_start: 0.8673 (pp) cc_final: 0.8461 (pp) REVERT: B 766 TYR cc_start: 0.8551 (m-80) cc_final: 0.8237 (m-10) REVERT: B 791 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8458 (mm-30) REVERT: B 818 GLU cc_start: 0.7752 (tt0) cc_final: 0.7256 (tt0) REVERT: B 821 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8163 (mmmt) REVERT: B 838 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8342 (tp40) REVERT: B 871 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7664 (p) REVERT: B 1121 LEU cc_start: 0.8289 (tt) cc_final: 0.7902 (mt) REVERT: C 27 ASP cc_start: 0.8124 (m-30) cc_final: 0.7599 (m-30) REVERT: C 59 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8357 (mp) REVERT: C 133 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.5996 (ptt90) REVERT: C 234 GLU cc_start: 0.8219 (pp20) cc_final: 0.7943 (pp20) REVERT: C 260 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8388 (tm-30) REVERT: D 39 MET cc_start: 0.9047 (tmm) cc_final: 0.8681 (tmm) REVERT: D 40 LEU cc_start: 0.9114 (mt) cc_final: 0.8781 (mt) REVERT: D 44 ARG cc_start: 0.9101 (tpp-160) cc_final: 0.8857 (tpt-90) REVERT: D 112 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7498 (mmtt) REVERT: E 18 MET cc_start: 0.8716 (mtt) cc_final: 0.8394 (mtp) REVERT: E 31 ASP cc_start: 0.9069 (p0) cc_final: 0.8795 (p0) REVERT: E 34 ASP cc_start: 0.8822 (m-30) cc_final: 0.8523 (p0) REVERT: E 72 MET cc_start: 0.7812 (ttp) cc_final: 0.7358 (ttp) REVERT: E 73 PHE cc_start: 0.8104 (t80) cc_final: 0.7593 (t80) REVERT: E 75 PHE cc_start: 0.8331 (t80) cc_final: 0.8105 (t80) REVERT: F 61 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8118 (mt-10) REVERT: F 121 ASP cc_start: 0.8281 (p0) cc_final: 0.8012 (p0) REVERT: G 3 TYR cc_start: 0.8308 (m-80) cc_final: 0.7910 (m-10) REVERT: G 21 ASN cc_start: 0.8185 (p0) cc_final: 0.7854 (p0) REVERT: G 24 ASN cc_start: 0.9134 (t0) cc_final: 0.8709 (t0) REVERT: G 33 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8300 (tm-30) REVERT: G 42 TYR cc_start: 0.9039 (m-80) cc_final: 0.8457 (m-10) REVERT: G 73 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8830 (tppt) REVERT: H 21 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8190 (tmtt) REVERT: H 29 HIS cc_start: 0.8140 (m170) cc_final: 0.7897 (m170) REVERT: H 33 GLU cc_start: 0.9134 (pm20) cc_final: 0.8650 (pm20) REVERT: H 35 PHE cc_start: 0.8809 (m-10) cc_final: 0.8338 (m-10) REVERT: H 36 LYS cc_start: 0.7800 (pttm) cc_final: 0.6117 (tptt) REVERT: H 37 MET cc_start: 0.7764 (mpp) cc_final: 0.7187 (mpp) REVERT: H 57 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.7238 (ttt-90) REVERT: H 66 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: H 95 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7695 (ttmm) REVERT: I 40 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7380 (tpp-160) REVERT: I 41 ASN cc_start: 0.8272 (p0) cc_final: 0.6720 (p0) REVERT: I 95 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7508 (m) REVERT: J 12 LYS cc_start: 0.9202 (ttpt) cc_final: 0.8994 (ttmm) REVERT: J 30 THR cc_start: 0.7683 (t) cc_final: 0.7444 (t) REVERT: J 48 MET cc_start: 0.9089 (tpp) cc_final: 0.8433 (tpp) REVERT: J 53 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7936 (p) REVERT: J 62 TYR cc_start: 0.8560 (m-80) cc_final: 0.8046 (m-80) REVERT: K 110 LYS cc_start: 0.8623 (tptp) cc_final: 0.8199 (tptp) REVERT: M 46 ILE cc_start: 0.3707 (OUTLIER) cc_final: 0.2613 (pp) REVERT: M 52 TRP cc_start: 0.4466 (t60) cc_final: 0.3159 (t60) REVERT: M 83 MET cc_start: 0.7943 (ptp) cc_final: 0.7526 (pmm) REVERT: M 116 ASN cc_start: 0.8706 (m-40) cc_final: 0.7487 (m-40) REVERT: M 120 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7408 (mm-30) REVERT: M 181 CYS cc_start: 0.8781 (t) cc_final: 0.8563 (t) REVERT: M 229 GLN cc_start: 0.9540 (tp40) cc_final: 0.8688 (tp40) REVERT: M 258 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8966 (mm) REVERT: M 300 PHE cc_start: 0.8059 (m-80) cc_final: 0.7511 (t80) REVERT: N 51 MET cc_start: 0.8081 (mmm) cc_final: 0.7707 (mmm) REVERT: N 312 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6412 (tm-30) REVERT: N 339 TYR cc_start: 0.8799 (p90) cc_final: 0.8357 (p90) REVERT: N 341 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8473 (pptt) REVERT: N 344 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8134 (tmm160) REVERT: N 348 LYS cc_start: 0.9499 (mmmt) cc_final: 0.9072 (mmmt) REVERT: N 349 TRP cc_start: 0.8365 (m-90) cc_final: 0.8003 (m-90) REVERT: N 350 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8366 (tppt) REVERT: O 27 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8418 (tm-30) REVERT: O 57 ASN cc_start: 0.9200 (m110) cc_final: 0.8415 (t0) REVERT: O 59 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8758 (mmm-85) REVERT: O 67 PHE cc_start: 0.8734 (t80) cc_final: 0.8107 (t80) REVERT: P 166 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: P 189 ASN cc_start: 0.7245 (t0) cc_final: 0.6455 (t0) REVERT: P 288 PHE cc_start: 0.7698 (t80) cc_final: 0.7455 (t80) REVERT: Q 45 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8840 (pm20) REVERT: Q 48 MET cc_start: 0.8435 (mmm) cc_final: 0.8150 (mmt) REVERT: Q 76 MET cc_start: 0.7458 (mmp) cc_final: 0.5907 (tpt) REVERT: Q 93 PHE cc_start: 0.7658 (m-80) cc_final: 0.7277 (m-10) REVERT: Q 96 TYR cc_start: 0.8155 (m-80) cc_final: 0.7481 (m-80) REVERT: R 120 MET cc_start: 0.7493 (mmm) cc_final: 0.7265 (mmp) REVERT: R 228 MET cc_start: 0.7915 (mmm) cc_final: 0.6817 (tpt) REVERT: S 26 TYR cc_start: 0.8504 (m-80) cc_final: 0.8277 (m-80) REVERT: S 96 GLN cc_start: 0.7108 (mp10) cc_final: 0.6823 (mp10) REVERT: S 110 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.5751 (t80) REVERT: S 153 ARG cc_start: 0.7459 (tpp80) cc_final: 0.6666 (tpp80) REVERT: S 168 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.7817 (p0) REVERT: T 56 PHE cc_start: 0.7713 (t80) cc_final: 0.7251 (t80) REVERT: T 186 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8442 (ttm) REVERT: T 212 TYR cc_start: 0.8848 (t80) cc_final: 0.8646 (t80) outliers start: 272 outliers final: 187 residues processed: 1275 average time/residue: 0.2395 time to fit residues: 502.0643 Evaluate side-chains 1266 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 1053 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 992 LYS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1161 GLU Chi-restraints excluded: chain C residue 7 PRO Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 258 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 312 GLU Chi-restraints excluded: chain N residue 341 LYS Chi-restraints excluded: chain N residue 344 ARG Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 40 PHE Chi-restraints excluded: chain O residue 63 ASN Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 166 GLN Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 60 ARG Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 198 ASN Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 110 PHE Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 168 ASN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 95 VAL Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 186 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 459 optimal weight: 0.1980 chunk 308 optimal weight: 0.0980 chunk 192 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 378 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 329 optimal weight: 7.9990 chunk 428 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 467 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 601 ASN A 735 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 ASN M 287 GLN P 166 GLN ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.148065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.096663 restraints weight = 102825.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.098019 restraints weight = 63050.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098346 restraints weight = 46013.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099155 restraints weight = 42657.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099218 restraints weight = 37750.448| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 47913 Z= 0.209 Angle : 0.808 18.896 65405 Z= 0.418 Chirality : 0.047 0.350 7284 Planarity : 0.006 0.176 7920 Dihedral : 17.933 177.713 7721 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.73 % Favored : 91.60 % Rotamer: Outliers : 5.92 % Allowed : 21.13 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.02 % Twisted Proline : 0.82 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.75 (0.11), residues: 5357 helix: 0.65 (0.12), residues: 1917 sheet: -0.11 (0.19), residues: 735 loop : -1.48 (0.12), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG S 108 TYR 0.036 0.002 TYR B 752 PHE 0.032 0.002 PHE Q 71 TRP 0.080 0.003 TRP T 31 HIS 0.007 0.001 HIS B 577 Details of bonding type rmsd covalent geometry : bond 0.00478 (47907) covalent geometry : angle 0.80803 (65405) hydrogen bonds : bond 0.04744 ( 2010) hydrogen bonds : angle 5.36478 ( 5613) metal coordination : bond 0.00360 ( 5) Misc. bond : bond 0.00100 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 283 poor density : 1098 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8592 (tp-100) cc_final: 0.8332 (tp-100) REVERT: A 108 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7678 (ttm-80) REVERT: A 212 LYS cc_start: 0.5911 (mmtp) cc_final: 0.4925 (mmmt) REVERT: A 233 CYS cc_start: 0.9013 (m) cc_final: 0.8508 (t) REVERT: A 242 TYR cc_start: 0.8654 (m-80) cc_final: 0.8235 (m-80) REVERT: A 266 MET cc_start: 0.7822 (tmm) cc_final: 0.7462 (tmm) REVERT: A 282 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8725 (m-30) REVERT: A 305 GLU cc_start: 0.8618 (tp30) cc_final: 0.8350 (tp30) REVERT: A 592 PHE cc_start: 0.8918 (t80) cc_final: 0.8683 (t80) REVERT: A 606 HIS cc_start: 0.3668 (OUTLIER) cc_final: 0.2754 (p90) REVERT: A 683 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7344 (tp30) REVERT: A 733 LEU cc_start: 0.9213 (mm) cc_final: 0.8897 (mm) REVERT: A 742 ASN cc_start: 0.8757 (t0) cc_final: 0.8103 (m-40) REVERT: A 869 GLU cc_start: 0.7764 (pt0) cc_final: 0.7239 (pt0) REVERT: A 876 ASP cc_start: 0.9114 (p0) cc_final: 0.8865 (p0) REVERT: A 955 GLU cc_start: 0.8649 (tp30) cc_final: 0.8199 (tp30) REVERT: A 959 MET cc_start: 0.7989 (mtt) cc_final: 0.7732 (mtt) REVERT: A 964 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7987 (tm-30) REVERT: A 1004 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8408 (mt) REVERT: A 1071 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7648 (mp0) REVERT: A 1086 MET cc_start: 0.9216 (mmm) cc_final: 0.8798 (tpp) REVERT: A 1094 SER cc_start: 0.9074 (m) cc_final: 0.8727 (p) REVERT: A 1212 LEU cc_start: 0.9230 (tp) cc_final: 0.8949 (mt) REVERT: A 1259 ILE cc_start: 0.9492 (mm) cc_final: 0.9286 (mm) REVERT: A 1306 LYS cc_start: 0.5842 (OUTLIER) cc_final: 0.5316 (ptmt) REVERT: A 1320 ILE cc_start: 0.8997 (mm) cc_final: 0.8545 (tp) REVERT: A 1332 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7552 (tp40) REVERT: A 1412 MET cc_start: 0.8528 (ttp) cc_final: 0.7739 (ppp) REVERT: A 1441 GLU cc_start: 0.7962 (tp30) cc_final: 0.7697 (tp30) REVERT: A 1463 LEU cc_start: 0.8192 (tp) cc_final: 0.7919 (mp) REVERT: A 1476 ASP cc_start: 0.8503 (t0) cc_final: 0.8217 (t0) REVERT: A 1479 LYS cc_start: 0.8383 (mmtm) cc_final: 0.7986 (tptt) REVERT: B 45 ASP cc_start: 0.8317 (m-30) cc_final: 0.7963 (m-30) REVERT: B 85 LEU cc_start: 0.9191 (tp) cc_final: 0.8957 (tp) REVERT: B 89 GLU cc_start: 0.7734 (tp30) cc_final: 0.7335 (tp30) REVERT: B 100 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 111 ASN cc_start: 0.8622 (m-40) cc_final: 0.8260 (m-40) REVERT: B 144 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.5511 (p-80) REVERT: B 155 MET cc_start: 0.8355 (ttm) cc_final: 0.8143 (ttp) REVERT: B 176 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7502 (mm-30) REVERT: B 250 SER cc_start: 0.4190 (OUTLIER) cc_final: 0.3849 (t) REVERT: B 324 ARG cc_start: 0.8471 (mmm160) cc_final: 0.7911 (mmm160) REVERT: B 363 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8779 (t80) REVERT: B 388 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8171 (m-10) REVERT: B 405 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8279 (ttm170) REVERT: B 422 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7911 (t80) REVERT: B 441 SER cc_start: 0.8473 (m) cc_final: 0.7880 (p) REVERT: B 677 MET cc_start: 0.9249 (tpp) cc_final: 0.8766 (tpp) REVERT: B 733 MET cc_start: 0.7889 (ptm) cc_final: 0.7646 (ptm) REVERT: B 737 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8352 (pp) REVERT: B 766 TYR cc_start: 0.8539 (m-80) cc_final: 0.8200 (m-10) REVERT: B 791 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8574 (mm-30) REVERT: B 818 GLU cc_start: 0.7647 (tt0) cc_final: 0.7167 (tt0) REVERT: B 820 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8502 (tppt) REVERT: B 889 LYS cc_start: 0.8209 (ptpt) cc_final: 0.8005 (ptpp) REVERT: B 1121 LEU cc_start: 0.8316 (tt) cc_final: 0.7903 (mt) REVERT: B 1130 THR cc_start: 0.5978 (OUTLIER) cc_final: 0.5742 (p) REVERT: B 1150 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7807 (mmm-85) REVERT: C 59 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8403 (mp) REVERT: C 133 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.5811 (ptt90) REVERT: C 182 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9204 (t) REVERT: C 234 GLU cc_start: 0.8306 (pp20) cc_final: 0.7783 (pp20) REVERT: C 260 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8389 (tm-30) REVERT: D 39 MET cc_start: 0.9050 (tmm) cc_final: 0.8695 (tmm) REVERT: D 40 LEU cc_start: 0.9173 (mt) cc_final: 0.8816 (mt) REVERT: D 44 ARG cc_start: 0.9173 (tpp-160) cc_final: 0.8458 (tpp-160) REVERT: D 112 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7636 (mmtt) REVERT: E 18 MET cc_start: 0.8740 (mtt) cc_final: 0.8397 (mtp) REVERT: E 72 MET cc_start: 0.7864 (ttp) cc_final: 0.7372 (ttp) REVERT: E 73 PHE cc_start: 0.8010 (t80) cc_final: 0.7480 (t80) REVERT: E 108 GLN cc_start: 0.8128 (tp40) cc_final: 0.7746 (tp-100) REVERT: F 61 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8103 (mt-10) REVERT: F 121 ASP cc_start: 0.8190 (p0) cc_final: 0.7836 (p0) REVERT: G 3 TYR cc_start: 0.8355 (m-80) cc_final: 0.7984 (m-10) REVERT: G 21 ASN cc_start: 0.8178 (p0) cc_final: 0.7825 (p0) REVERT: G 24 ASN cc_start: 0.9133 (t0) cc_final: 0.8719 (t0) REVERT: G 33 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8326 (tm-30) REVERT: G 42 TYR cc_start: 0.9117 (m-80) cc_final: 0.8545 (m-10) REVERT: G 73 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8706 (tptp) REVERT: H 20 LYS cc_start: 0.3492 (pttt) cc_final: 0.3153 (ttpp) REVERT: H 21 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8109 (tmtt) REVERT: H 33 GLU cc_start: 0.9115 (pm20) cc_final: 0.8682 (pm20) REVERT: H 35 PHE cc_start: 0.8763 (m-10) cc_final: 0.8405 (m-10) REVERT: H 66 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: H 95 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7693 (ttmm) REVERT: I 1 MET cc_start: 0.0153 (mtt) cc_final: -0.1130 (mtt) REVERT: I 27 LYS cc_start: 0.6716 (mmtm) cc_final: 0.6369 (mmtm) REVERT: I 40 ARG cc_start: 0.7942 (mmm160) cc_final: 0.7553 (mmm160) REVERT: I 41 ASN cc_start: 0.8196 (p0) cc_final: 0.7625 (p0) REVERT: I 63 ASP cc_start: 0.6385 (p0) cc_final: 0.5821 (p0) REVERT: I 67 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: I 95 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7620 (m) REVERT: J 30 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7154 (t) REVERT: J 48 MET cc_start: 0.9042 (tpp) cc_final: 0.8359 (tpp) REVERT: J 53 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7980 (p) REVERT: J 62 TYR cc_start: 0.8529 (m-80) cc_final: 0.8016 (m-80) REVERT: M 52 TRP cc_start: 0.4779 (t60) cc_final: 0.3946 (t60) REVERT: M 107 MET cc_start: 0.8034 (pmm) cc_final: 0.7749 (pmm) REVERT: M 116 ASN cc_start: 0.8765 (m-40) cc_final: 0.7687 (m-40) REVERT: M 139 ASN cc_start: 0.9338 (m-40) cc_final: 0.8574 (m110) REVERT: M 181 CYS cc_start: 0.8745 (t) cc_final: 0.8525 (t) REVERT: M 227 GLN cc_start: 0.7814 (tp40) cc_final: 0.7432 (tp40) REVERT: M 229 GLN cc_start: 0.9523 (OUTLIER) cc_final: 0.8671 (tp40) REVERT: M 258 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8984 (mm) REVERT: N 51 MET cc_start: 0.8108 (mmm) cc_final: 0.7657 (mmm) REVERT: N 312 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6298 (mm-30) REVERT: N 339 TYR cc_start: 0.8953 (p90) cc_final: 0.8515 (p90) REVERT: N 341 LYS cc_start: 0.8823 (pttp) cc_final: 0.7645 (pttp) REVERT: N 344 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7882 (tmm160) REVERT: N 348 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9166 (mmmt) REVERT: N 349 TRP cc_start: 0.8491 (m-90) cc_final: 0.7984 (m-90) REVERT: N 350 LYS cc_start: 0.9062 (mmtm) cc_final: 0.8542 (tppt) REVERT: O 57 ASN cc_start: 0.9260 (m110) cc_final: 0.8471 (t0) REVERT: O 67 PHE cc_start: 0.8808 (t80) cc_final: 0.8081 (t80) REVERT: O 82 ARG cc_start: 0.9140 (mpp80) cc_final: 0.8819 (mtm-85) REVERT: P 189 ASN cc_start: 0.7717 (t0) cc_final: 0.6900 (t0) REVERT: P 288 PHE cc_start: 0.7807 (t80) cc_final: 0.7442 (t80) REVERT: P 325 PHE cc_start: 0.8601 (t80) cc_final: 0.8340 (t80) REVERT: Q 48 MET cc_start: 0.8259 (mmm) cc_final: 0.7981 (mmt) REVERT: Q 76 MET cc_start: 0.7212 (mmp) cc_final: 0.5887 (tpt) REVERT: Q 93 PHE cc_start: 0.7632 (m-80) cc_final: 0.7225 (m-10) REVERT: Q 96 TYR cc_start: 0.8334 (m-80) cc_final: 0.8064 (m-80) REVERT: R 120 MET cc_start: 0.7644 (mmm) cc_final: 0.7364 (mmp) REVERT: R 228 MET cc_start: 0.8070 (mmm) cc_final: 0.6982 (tpt) REVERT: S 14 TYR cc_start: 0.8577 (m-80) cc_final: 0.8307 (t80) REVERT: S 26 TYR cc_start: 0.8617 (m-80) cc_final: 0.8376 (m-80) REVERT: S 36 LYS cc_start: 0.9322 (mtmm) cc_final: 0.8573 (tptp) REVERT: S 96 GLN cc_start: 0.7036 (mp10) cc_final: 0.6397 (mp10) REVERT: S 168 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.7861 (p0) REVERT: S 177 MET cc_start: 0.8422 (mmm) cc_final: 0.7083 (ttt) REVERT: T 56 PHE cc_start: 0.7934 (t80) cc_final: 0.7183 (t80) REVERT: T 186 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8516 (ttm) outliers start: 283 outliers final: 194 residues processed: 1269 average time/residue: 0.2013 time to fit residues: 422.6619 Evaluate side-chains 1265 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 1043 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1445 HIS Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 820 LYS Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1058 LYS Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1161 GLU Chi-restraints excluded: chain C residue 7 PRO Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 258 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 312 GLU Chi-restraints excluded: chain N residue 344 ARG Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 365 TYR Chi-restraints excluded: chain O residue 40 PHE Chi-restraints excluded: chain O residue 63 ASN Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 166 GLN Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 71 PHE Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 198 ASN Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 168 ASN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 186 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 258 optimal weight: 2.9990 chunk 539 optimal weight: 30.0000 chunk 314 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 390 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 456 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 423 optimal weight: 3.9990 chunk 488 optimal weight: 0.6980 chunk 428 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 GLN ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 GLN ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 GLN S 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.147499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096684 restraints weight = 103054.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097661 restraints weight = 63100.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097735 restraints weight = 45570.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098431 restraints weight = 46007.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098595 restraints weight = 38636.472| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 47913 Z= 0.233 Angle : 0.836 22.569 65405 Z= 0.431 Chirality : 0.048 0.427 7284 Planarity : 0.007 0.189 7920 Dihedral : 17.947 177.756 7721 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.23 % Favored : 91.15 % Rotamer: Outliers : 5.75 % Allowed : 22.51 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.82 (0.12), residues: 5357 helix: 0.60 (0.12), residues: 1922 sheet: -0.24 (0.19), residues: 741 loop : -1.51 (0.12), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG S 108 TYR 0.046 0.002 TYR G 167 PHE 0.038 0.002 PHE M 195 TRP 0.087 0.003 TRP T 31 HIS 0.008 0.001 HIS Q 109 Details of bonding type rmsd covalent geometry : bond 0.00537 (47907) covalent geometry : angle 0.83630 (65405) hydrogen bonds : bond 0.04798 ( 2010) hydrogen bonds : angle 5.43528 ( 5613) metal coordination : bond 0.00432 ( 5) Misc. bond : bond 0.00097 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 275 poor density : 1091 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8324 (tp-100) REVERT: A 108 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7931 (ttm-80) REVERT: A 212 LYS cc_start: 0.6232 (mmtp) cc_final: 0.5550 (mmtp) REVERT: A 233 CYS cc_start: 0.9035 (m) cc_final: 0.8521 (t) REVERT: A 242 TYR cc_start: 0.8653 (m-80) cc_final: 0.8380 (m-80) REVERT: A 266 MET cc_start: 0.7717 (tmm) cc_final: 0.7488 (tmm) REVERT: A 592 PHE cc_start: 0.8992 (t80) cc_final: 0.8773 (t80) REVERT: A 606 HIS cc_start: 0.3860 (OUTLIER) cc_final: 0.2909 (p90) REVERT: A 683 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7424 (tp30) REVERT: A 733 LEU cc_start: 0.9210 (mm) cc_final: 0.8876 (mm) REVERT: A 742 ASN cc_start: 0.8771 (t0) cc_final: 0.8078 (m-40) REVERT: A 749 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8515 (tmm-80) REVERT: A 869 GLU cc_start: 0.7795 (pt0) cc_final: 0.7339 (pt0) REVERT: A 876 ASP cc_start: 0.9166 (p0) cc_final: 0.8928 (p0) REVERT: A 955 GLU cc_start: 0.8567 (tp30) cc_final: 0.8089 (tp30) REVERT: A 959 MET cc_start: 0.8118 (mtt) cc_final: 0.7800 (mtt) REVERT: A 964 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 1004 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8397 (mt) REVERT: A 1086 MET cc_start: 0.9265 (mmm) cc_final: 0.8500 (tpp) REVERT: A 1094 SER cc_start: 0.9057 (m) cc_final: 0.8725 (p) REVERT: A 1212 LEU cc_start: 0.9239 (tp) cc_final: 0.8931 (mt) REVERT: A 1262 MET cc_start: 0.6799 (tpp) cc_final: 0.5014 (tpp) REVERT: A 1306 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5418 (ptmt) REVERT: A 1320 ILE cc_start: 0.9074 (mm) cc_final: 0.8625 (tp) REVERT: A 1332 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7606 (tp40) REVERT: A 1412 MET cc_start: 0.8494 (ttp) cc_final: 0.7744 (ppp) REVERT: A 1441 GLU cc_start: 0.7994 (tp30) cc_final: 0.7586 (tp30) REVERT: A 1463 LEU cc_start: 0.8291 (tp) cc_final: 0.7993 (mp) REVERT: A 1476 ASP cc_start: 0.8401 (t0) cc_final: 0.8055 (t0) REVERT: A 1479 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8072 (tptt) REVERT: A 1484 MET cc_start: 0.3477 (mtt) cc_final: 0.1945 (mtt) REVERT: B 45 ASP cc_start: 0.8358 (m-30) cc_final: 0.8033 (m-30) REVERT: B 85 LEU cc_start: 0.9237 (tp) cc_final: 0.9018 (tp) REVERT: B 87 LYS cc_start: 0.8493 (tttm) cc_final: 0.8290 (ttmm) REVERT: B 89 GLU cc_start: 0.7695 (tp30) cc_final: 0.7403 (tp30) REVERT: B 100 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 111 ASN cc_start: 0.8601 (m-40) cc_final: 0.8159 (m-40) REVERT: B 144 HIS cc_start: 0.6023 (OUTLIER) cc_final: 0.5592 (p-80) REVERT: B 176 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 250 SER cc_start: 0.4343 (OUTLIER) cc_final: 0.3941 (t) REVERT: B 324 ARG cc_start: 0.8478 (mmm160) cc_final: 0.7893 (mmm160) REVERT: B 363 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.8773 (t80) REVERT: B 388 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: B 405 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8267 (ttp-170) REVERT: B 422 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7833 (t80) REVERT: B 677 MET cc_start: 0.9248 (tpp) cc_final: 0.8804 (tpp) REVERT: B 737 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8360 (pp) REVERT: B 764 MET cc_start: 0.8489 (mmm) cc_final: 0.8237 (mmm) REVERT: B 766 TYR cc_start: 0.8631 (m-80) cc_final: 0.8413 (m-10) REVERT: B 791 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8600 (mm-30) REVERT: B 818 GLU cc_start: 0.7770 (tt0) cc_final: 0.7440 (tm-30) REVERT: B 1121 LEU cc_start: 0.8372 (tt) cc_final: 0.7972 (mt) REVERT: B 1130 THR cc_start: 0.5870 (OUTLIER) cc_final: 0.5635 (p) REVERT: C 59 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8408 (mp) REVERT: C 260 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 39 MET cc_start: 0.9112 (tmm) cc_final: 0.8745 (tmm) REVERT: D 40 LEU cc_start: 0.9136 (mt) cc_final: 0.8751 (mt) REVERT: D 44 ARG cc_start: 0.9105 (tpp-160) cc_final: 0.8490 (tpp-160) REVERT: D 112 LYS cc_start: 0.7607 (mmtt) cc_final: 0.7381 (mmtt) REVERT: E 9 ARG cc_start: 0.8967 (mtt180) cc_final: 0.8753 (mtt90) REVERT: E 18 MET cc_start: 0.8781 (mtt) cc_final: 0.8440 (mtp) REVERT: E 34 ASP cc_start: 0.8843 (m-30) cc_final: 0.8535 (p0) REVERT: E 72 MET cc_start: 0.7840 (ttp) cc_final: 0.7373 (ttp) REVERT: E 73 PHE cc_start: 0.8053 (t80) cc_final: 0.7437 (t80) REVERT: F 61 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8114 (mt-10) REVERT: F 121 ASP cc_start: 0.8287 (p0) cc_final: 0.7221 (p0) REVERT: G 3 TYR cc_start: 0.8530 (m-80) cc_final: 0.8071 (m-10) REVERT: G 4 HIS cc_start: 0.7926 (t-90) cc_final: 0.7653 (t70) REVERT: G 21 ASN cc_start: 0.8269 (p0) cc_final: 0.7889 (p0) REVERT: G 24 ASN cc_start: 0.9177 (t0) cc_final: 0.8739 (t0) REVERT: G 33 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8328 (tm-30) REVERT: G 73 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8632 (tppt) REVERT: G 164 MET cc_start: 0.8945 (mtt) cc_final: 0.8405 (mmm) REVERT: H 13 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8446 (mmtm) REVERT: H 21 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8152 (tmtt) REVERT: H 33 GLU cc_start: 0.9062 (pm20) cc_final: 0.8599 (pm20) REVERT: H 35 PHE cc_start: 0.8825 (m-10) cc_final: 0.8391 (m-10) REVERT: H 66 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: H 95 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7695 (ttmm) REVERT: I 1 MET cc_start: -0.0206 (mtt) cc_final: -0.1372 (mtt) REVERT: I 41 ASN cc_start: 0.8266 (p0) cc_final: 0.7717 (p0) REVERT: I 56 ASN cc_start: 0.8425 (p0) cc_final: 0.8064 (p0) REVERT: I 74 GLN cc_start: 0.8440 (mp10) cc_final: 0.8195 (mp10) REVERT: I 95 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7331 (m) REVERT: J 48 MET cc_start: 0.9106 (tpp) cc_final: 0.8430 (tpp) REVERT: J 62 TYR cc_start: 0.8548 (m-80) cc_final: 0.7970 (m-80) REVERT: M 116 ASN cc_start: 0.8663 (m-40) cc_final: 0.7917 (m110) REVERT: M 139 ASN cc_start: 0.9354 (m-40) cc_final: 0.9033 (m110) REVERT: M 181 CYS cc_start: 0.8756 (t) cc_final: 0.8535 (t) REVERT: M 193 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8687 (ttm170) REVERT: M 229 GLN cc_start: 0.9583 (tp40) cc_final: 0.8930 (tp40) REVERT: M 258 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9036 (mm) REVERT: M 300 PHE cc_start: 0.7987 (m-80) cc_final: 0.7425 (t80) REVERT: N 51 MET cc_start: 0.8076 (mmm) cc_final: 0.7750 (mmm) REVERT: N 339 TYR cc_start: 0.8956 (p90) cc_final: 0.8401 (p90) REVERT: N 344 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7916 (tmm160) REVERT: N 348 LYS cc_start: 0.9542 (mmmt) cc_final: 0.9325 (mmmt) REVERT: N 349 TRP cc_start: 0.8495 (m-90) cc_final: 0.8279 (m-90) REVERT: O 57 ASN cc_start: 0.9246 (m110) cc_final: 0.8349 (t0) REVERT: O 67 PHE cc_start: 0.8887 (t80) cc_final: 0.8240 (t80) REVERT: O 82 ARG cc_start: 0.9128 (mpp80) cc_final: 0.8141 (mpp80) REVERT: P 189 ASN cc_start: 0.7809 (t0) cc_final: 0.6938 (t0) REVERT: P 288 PHE cc_start: 0.7793 (t80) cc_final: 0.7523 (t80) REVERT: P 325 PHE cc_start: 0.8564 (t80) cc_final: 0.8264 (t80) REVERT: Q 48 MET cc_start: 0.8151 (mmm) cc_final: 0.7898 (mmt) REVERT: Q 76 MET cc_start: 0.7006 (mmp) cc_final: 0.5626 (tpt) REVERT: Q 93 PHE cc_start: 0.7666 (m-80) cc_final: 0.7213 (m-10) REVERT: Q 96 TYR cc_start: 0.8380 (m-80) cc_final: 0.8077 (m-80) REVERT: R 228 MET cc_start: 0.8119 (mmm) cc_final: 0.7082 (tpt) REVERT: S 14 TYR cc_start: 0.8501 (m-80) cc_final: 0.8212 (t80) REVERT: S 26 TYR cc_start: 0.8631 (m-80) cc_final: 0.8402 (m-80) REVERT: S 36 LYS cc_start: 0.9299 (mtmm) cc_final: 0.8550 (tptp) REVERT: S 96 GLN cc_start: 0.7122 (mp10) cc_final: 0.6601 (mp10) REVERT: S 110 PHE cc_start: 0.8576 (t80) cc_final: 0.6991 (t80) REVERT: S 144 TYR cc_start: 0.8397 (m-80) cc_final: 0.8191 (m-80) REVERT: S 168 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8144 (m-40) REVERT: S 177 MET cc_start: 0.8223 (mmm) cc_final: 0.6912 (ttt) REVERT: T 56 PHE cc_start: 0.7740 (t80) cc_final: 0.7297 (t80) REVERT: T 130 LEU cc_start: 0.9352 (mt) cc_final: 0.9052 (pp) REVERT: T 186 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8526 (ttm) outliers start: 275 outliers final: 213 residues processed: 1249 average time/residue: 0.1826 time to fit residues: 377.7723 Evaluate side-chains 1262 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 1029 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1391 SER Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1445 HIS Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1058 LYS Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1161 GLU Chi-restraints excluded: chain C residue 7 PRO Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 193 ARG Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 258 ILE Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 312 GLU Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 344 ARG Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 365 TYR Chi-restraints excluded: chain O residue 63 ASN Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 71 PHE Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 198 ASN Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 29 MET Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 168 ASN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 186 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 333 optimal weight: 8.9990 chunk 242 optimal weight: 0.5980 chunk 542 optimal weight: 4.9990 chunk 486 optimal weight: 10.0000 chunk 331 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 532 optimal weight: 5.9990 chunk 444 optimal weight: 0.4980 chunk 459 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS A 485 ASN A 673 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN I 46 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN N 343 HIS ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.147018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093828 restraints weight = 103322.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096782 restraints weight = 57506.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098640 restraints weight = 40771.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099745 restraints weight = 33482.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100351 restraints weight = 30011.629| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 47913 Z= 0.245 Angle : 0.858 17.795 65405 Z= 0.443 Chirality : 0.049 0.496 7284 Planarity : 0.007 0.170 7920 Dihedral : 17.969 177.660 7717 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.42 % Favored : 90.95 % Rotamer: Outliers : 5.60 % Allowed : 23.10 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.94 (0.11), residues: 5357 helix: 0.48 (0.12), residues: 1929 sheet: -0.46 (0.19), residues: 768 loop : -1.52 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG S 108 TYR 0.039 0.002 TYR G 167 PHE 0.047 0.002 PHE R 139 TRP 0.093 0.003 TRP T 31 HIS 0.014 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00563 (47907) covalent geometry : angle 0.85783 (65405) hydrogen bonds : bond 0.04863 ( 2010) hydrogen bonds : angle 5.46720 ( 5613) metal coordination : bond 0.00419 ( 5) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 1073 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8390 (tp-100) REVERT: A 108 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7926 (ttm-80) REVERT: A 212 LYS cc_start: 0.6176 (mmtp) cc_final: 0.5517 (mmtp) REVERT: A 233 CYS cc_start: 0.8933 (m) cc_final: 0.8528 (t) REVERT: A 242 TYR cc_start: 0.8652 (m-80) cc_final: 0.8179 (m-80) REVERT: A 606 HIS cc_start: 0.3960 (OUTLIER) cc_final: 0.3083 (p90) REVERT: A 660 MET cc_start: 0.8110 (mmm) cc_final: 0.7860 (mmm) REVERT: A 733 LEU cc_start: 0.9198 (mm) cc_final: 0.8869 (mm) REVERT: A 742 ASN cc_start: 0.8766 (t0) cc_final: 0.8081 (m-40) REVERT: A 749 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8422 (ttp80) REVERT: A 876 ASP cc_start: 0.9171 (p0) cc_final: 0.8947 (p0) REVERT: A 955 GLU cc_start: 0.8376 (tp30) cc_final: 0.7901 (tp30) REVERT: A 959 MET cc_start: 0.8050 (mtt) cc_final: 0.7444 (mtt) REVERT: A 1004 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 1086 MET cc_start: 0.9307 (mmm) cc_final: 0.8638 (tpp) REVERT: A 1094 SER cc_start: 0.9075 (m) cc_final: 0.8753 (p) REVERT: A 1228 MET cc_start: 0.8781 (mmp) cc_final: 0.8191 (mmm) REVERT: A 1262 MET cc_start: 0.6782 (tpp) cc_final: 0.5404 (tpp) REVERT: A 1269 MET cc_start: 0.8377 (pmm) cc_final: 0.7956 (pmm) REVERT: A 1306 LYS cc_start: 0.5984 (OUTLIER) cc_final: 0.5500 (ptmt) REVERT: A 1320 ILE cc_start: 0.9092 (mm) cc_final: 0.8509 (tp) REVERT: A 1332 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7856 (tp40) REVERT: A 1412 MET cc_start: 0.8496 (ttp) cc_final: 0.7760 (ppp) REVERT: A 1441 GLU cc_start: 0.8013 (tp30) cc_final: 0.7628 (tp30) REVERT: A 1463 LEU cc_start: 0.8236 (tp) cc_final: 0.8002 (mp) REVERT: A 1476 ASP cc_start: 0.8436 (t0) cc_final: 0.8148 (t0) REVERT: A 1479 LYS cc_start: 0.8378 (mmtm) cc_final: 0.8130 (tptt) REVERT: A 1484 MET cc_start: 0.3299 (mtt) cc_final: 0.1765 (mtt) REVERT: B 45 ASP cc_start: 0.8340 (m-30) cc_final: 0.8063 (m-30) REVERT: B 85 LEU cc_start: 0.9233 (tp) cc_final: 0.9027 (tp) REVERT: B 87 LYS cc_start: 0.8480 (tttm) cc_final: 0.8229 (ttmm) REVERT: B 89 GLU cc_start: 0.7691 (tp30) cc_final: 0.7434 (tp30) REVERT: B 100 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 144 HIS cc_start: 0.6026 (OUTLIER) cc_final: 0.5570 (p-80) REVERT: B 176 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 264 LYS cc_start: 0.8096 (mttm) cc_final: 0.7747 (mttm) REVERT: B 324 ARG cc_start: 0.8435 (mmm160) cc_final: 0.7844 (mmm160) REVERT: B 363 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8664 (t80) REVERT: B 388 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: B 405 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8366 (ttp-170) REVERT: B 674 MET cc_start: 0.9392 (tpt) cc_final: 0.8924 (tpp) REVERT: B 677 MET cc_start: 0.9236 (tpp) cc_final: 0.8805 (tpp) REVERT: B 737 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8353 (pp) REVERT: B 764 MET cc_start: 0.8475 (mmm) cc_final: 0.8240 (mmm) REVERT: B 766 TYR cc_start: 0.8649 (m-80) cc_final: 0.8409 (m-10) REVERT: B 791 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8595 (mm-30) REVERT: B 818 GLU cc_start: 0.7823 (tt0) cc_final: 0.7230 (tm-30) REVERT: B 1121 LEU cc_start: 0.8379 (tt) cc_final: 0.7943 (mt) REVERT: B 1130 THR cc_start: 0.6006 (OUTLIER) cc_final: 0.5759 (p) REVERT: B 1150 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7472 (mtp180) REVERT: C 59 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8440 (mp) REVERT: C 260 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8295 (tm-30) REVERT: D 39 MET cc_start: 0.9161 (tmm) cc_final: 0.8854 (tmm) REVERT: D 40 LEU cc_start: 0.9182 (mt) cc_final: 0.8792 (mt) REVERT: D 44 ARG cc_start: 0.9149 (tpp-160) cc_final: 0.8483 (tpp-160) REVERT: D 66 ASN cc_start: 0.9319 (m110) cc_final: 0.9015 (p0) REVERT: D 112 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7507 (mmtt) REVERT: E 18 MET cc_start: 0.8738 (mtt) cc_final: 0.8363 (ttm) REVERT: E 31 ASP cc_start: 0.9080 (p0) cc_final: 0.8867 (p0) REVERT: E 34 ASP cc_start: 0.8704 (m-30) cc_final: 0.8427 (p0) REVERT: E 72 MET cc_start: 0.7754 (ttp) cc_final: 0.7356 (ttp) REVERT: E 73 PHE cc_start: 0.7926 (t80) cc_final: 0.7304 (t80) REVERT: E 192 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8462 (ptmm) REVERT: F 61 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8173 (mt-10) REVERT: F 121 ASP cc_start: 0.8148 (p0) cc_final: 0.7906 (p0) REVERT: G 3 TYR cc_start: 0.8448 (m-80) cc_final: 0.8029 (m-10) REVERT: G 21 ASN cc_start: 0.8154 (p0) cc_final: 0.7815 (p0) REVERT: G 24 ASN cc_start: 0.9105 (t0) cc_final: 0.8680 (t0) REVERT: G 33 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8260 (tm-30) REVERT: G 60 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6823 (tm-30) REVERT: G 164 MET cc_start: 0.8977 (mtt) cc_final: 0.8460 (mmm) REVERT: H 33 GLU cc_start: 0.8815 (pm20) cc_final: 0.8498 (pm20) REVERT: H 35 PHE cc_start: 0.8634 (m-10) cc_final: 0.8094 (m-10) REVERT: H 36 LYS cc_start: 0.7663 (pttm) cc_final: 0.6565 (tptt) REVERT: H 37 MET cc_start: 0.7137 (mpp) cc_final: 0.6254 (mmt) REVERT: H 66 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: H 95 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7750 (ttmm) REVERT: I 1 MET cc_start: -0.0185 (mtt) cc_final: -0.1440 (mtt) REVERT: I 24 LEU cc_start: 0.6580 (mp) cc_final: 0.6155 (mp) REVERT: I 40 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7780 (mmm160) REVERT: I 41 ASN cc_start: 0.8193 (p0) cc_final: 0.7256 (p0) REVERT: I 95 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7318 (m) REVERT: J 19 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6949 (tm-30) REVERT: J 48 MET cc_start: 0.9108 (tpp) cc_final: 0.8397 (tpp) REVERT: J 62 TYR cc_start: 0.8536 (m-80) cc_final: 0.8006 (m-80) REVERT: K 68 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7922 (mm-30) REVERT: M 112 ARG cc_start: 0.8087 (tpp-160) cc_final: 0.7394 (mmt-90) REVERT: M 116 ASN cc_start: 0.8673 (m-40) cc_final: 0.8036 (m110) REVERT: M 139 ASN cc_start: 0.9345 (m-40) cc_final: 0.8999 (m110) REVERT: M 154 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7135 (mpt180) REVERT: M 181 CYS cc_start: 0.8731 (t) cc_final: 0.8499 (t) REVERT: M 193 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8834 (ttm170) REVERT: M 229 GLN cc_start: 0.9572 (tp40) cc_final: 0.8648 (tp40) REVERT: M 258 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9064 (mm) REVERT: M 300 PHE cc_start: 0.7787 (m-80) cc_final: 0.7299 (t80) REVERT: N 51 MET cc_start: 0.8050 (mmm) cc_final: 0.7664 (mmm) REVERT: N 339 TYR cc_start: 0.8891 (p90) cc_final: 0.8363 (p90) REVERT: N 344 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7742 (ttp80) REVERT: N 348 LYS cc_start: 0.9510 (mmmt) cc_final: 0.9237 (mmmt) REVERT: N 349 TRP cc_start: 0.8465 (m-90) cc_final: 0.8239 (m-90) REVERT: N 363 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8748 (mtm-85) REVERT: O 57 ASN cc_start: 0.9109 (m110) cc_final: 0.8551 (t0) REVERT: O 67 PHE cc_start: 0.8871 (t80) cc_final: 0.8304 (t80) REVERT: P 189 ASN cc_start: 0.7767 (t0) cc_final: 0.6902 (t0) REVERT: P 283 TYR cc_start: 0.7213 (t80) cc_final: 0.6902 (t80) REVERT: P 288 PHE cc_start: 0.7730 (t80) cc_final: 0.7457 (t80) REVERT: P 325 PHE cc_start: 0.8479 (t80) cc_final: 0.8194 (t80) REVERT: Q 48 MET cc_start: 0.8154 (mmm) cc_final: 0.7887 (mmt) REVERT: Q 76 MET cc_start: 0.7042 (mmp) cc_final: 0.5914 (tpt) REVERT: Q 93 PHE cc_start: 0.7684 (m-80) cc_final: 0.7215 (m-10) REVERT: Q 96 TYR cc_start: 0.8460 (m-80) cc_final: 0.8163 (m-80) REVERT: R 228 MET cc_start: 0.8178 (mmm) cc_final: 0.7275 (tpt) REVERT: S 14 TYR cc_start: 0.8684 (m-80) cc_final: 0.8366 (t80) REVERT: S 36 LYS cc_start: 0.9268 (mtmm) cc_final: 0.8498 (tptp) REVERT: S 39 PHE cc_start: 0.8575 (m-10) cc_final: 0.8324 (m-10) REVERT: S 96 GLN cc_start: 0.7137 (mp10) cc_final: 0.6565 (mp10) REVERT: S 110 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7568 (t80) REVERT: S 168 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8292 (m-40) REVERT: S 173 HIS cc_start: 0.6728 (p90) cc_final: 0.6002 (m-70) REVERT: S 177 MET cc_start: 0.8165 (mmm) cc_final: 0.6943 (ttt) REVERT: T 56 PHE cc_start: 0.7971 (t80) cc_final: 0.7361 (t80) REVERT: T 153 TYR cc_start: 0.6863 (t80) cc_final: 0.6493 (t80) REVERT: T 168 LYS cc_start: 0.8489 (mptt) cc_final: 0.8280 (mmtt) REVERT: T 186 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8501 (ttm) outliers start: 268 outliers final: 207 residues processed: 1226 average time/residue: 0.1796 time to fit residues: 364.7621 Evaluate side-chains 1266 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1039 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1306 LYS Chi-restraints excluded: chain A residue 1391 SER Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1445 HIS Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 631 GLN Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1058 LYS Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain B residue 1161 GLU Chi-restraints excluded: chain C residue 7 PRO Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 154 ARG Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 193 ARG Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 258 ILE Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 312 GLU Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 344 ARG Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 365 TYR Chi-restraints excluded: chain O residue 63 ASN Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 232 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 71 PHE Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 188 TYR Chi-restraints excluded: chain Q residue 198 ASN Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 29 MET Chi-restraints excluded: chain S residue 110 PHE Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 168 ASN Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 186 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 275 optimal weight: 2.9990 chunk 439 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 224 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 chunk 521 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B1129 ASN ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.147431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094669 restraints weight = 102842.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098829 restraints weight = 60815.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098831 restraints weight = 39861.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099564 restraints weight = 34835.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099974 restraints weight = 32598.504| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 47913 Z= 0.217 Angle : 0.856 17.082 65405 Z= 0.442 Chirality : 0.048 0.437 7284 Planarity : 0.006 0.167 7920 Dihedral : 17.983 177.444 7717 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.44 % Favored : 90.93 % Rotamer: Outliers : 5.20 % Allowed : 23.72 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.97 (0.12), residues: 5357 helix: 0.47 (0.12), residues: 1930 sheet: -0.54 (0.19), residues: 772 loop : -1.52 (0.12), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1167 TYR 0.037 0.002 TYR G 167 PHE 0.051 0.002 PHE R 139 TRP 0.080 0.003 TRP T 31 HIS 0.009 0.001 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00500 (47907) covalent geometry : angle 0.85634 (65405) hydrogen bonds : bond 0.04741 ( 2010) hydrogen bonds : angle 5.43147 ( 5613) metal coordination : bond 0.00343 ( 5) Misc. bond : bond 0.00083 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 1082 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8351 (tp-100) REVERT: A 108 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7993 (ttm-80) REVERT: A 143 HIS cc_start: 0.9337 (m-70) cc_final: 0.9104 (m-70) REVERT: A 145 TYR cc_start: 0.9159 (t80) cc_final: 0.8914 (t80) REVERT: A 212 LYS cc_start: 0.6456 (mmtp) cc_final: 0.5682 (mmtp) REVERT: A 233 CYS cc_start: 0.8784 (m) cc_final: 0.8355 (t) REVERT: A 242 TYR cc_start: 0.8696 (m-80) cc_final: 0.8090 (m-80) REVERT: A 321 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 341 GLN cc_start: 0.8747 (mm110) cc_final: 0.8545 (mm-40) REVERT: A 441 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: A 606 HIS cc_start: 0.4109 (OUTLIER) cc_final: 0.3208 (p90) REVERT: A 733 LEU cc_start: 0.9219 (mm) cc_final: 0.8888 (mm) REVERT: A 742 ASN cc_start: 0.8764 (t0) cc_final: 0.8079 (m-40) REVERT: A 749 ARG cc_start: 0.8996 (ttp80) cc_final: 0.8460 (ttp80) REVERT: A 876 ASP cc_start: 0.9151 (p0) cc_final: 0.8941 (p0) REVERT: A 955 GLU cc_start: 0.8448 (tp30) cc_final: 0.7896 (tp30) REVERT: A 959 MET cc_start: 0.8061 (mtt) cc_final: 0.7448 (mtt) REVERT: A 1004 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 1071 GLU cc_start: 0.7880 (mp0) cc_final: 0.7485 (mp0) REVERT: A 1086 MET cc_start: 0.9269 (mmm) cc_final: 0.8518 (tpp) REVERT: A 1094 SER cc_start: 0.9090 (m) cc_final: 0.8755 (p) REVERT: A 1132 LYS cc_start: 0.8827 (mttp) cc_final: 0.8585 (mttp) REVERT: A 1228 MET cc_start: 0.8812 (mmp) cc_final: 0.8218 (mmm) REVERT: A 1269 MET cc_start: 0.8461 (pmm) cc_final: 0.8113 (pmm) REVERT: A 1320 ILE cc_start: 0.9123 (mm) cc_final: 0.8683 (tp) REVERT: A 1332 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7915 (tp40) REVERT: A 1412 MET cc_start: 0.8384 (ttp) cc_final: 0.7669 (ppp) REVERT: A 1441 GLU cc_start: 0.7999 (tp30) cc_final: 0.7588 (tp30) REVERT: A 1463 LEU cc_start: 0.8202 (tp) cc_final: 0.7984 (mp) REVERT: A 1476 ASP cc_start: 0.8387 (t0) cc_final: 0.8009 (t0) REVERT: A 1484 MET cc_start: 0.3403 (mtt) cc_final: 0.1865 (mtt) REVERT: B 45 ASP cc_start: 0.8378 (m-30) cc_final: 0.8112 (m-30) REVERT: B 85 LEU cc_start: 0.9257 (tp) cc_final: 0.9036 (tp) REVERT: B 87 LYS cc_start: 0.8478 (tttm) cc_final: 0.8245 (ttmm) REVERT: B 144 HIS cc_start: 0.6071 (OUTLIER) cc_final: 0.5638 (p-80) REVERT: B 176 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7263 (mm-30) REVERT: B 264 LYS cc_start: 0.8183 (mttm) cc_final: 0.7903 (mttm) REVERT: B 363 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8645 (t80) REVERT: B 388 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: B 422 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7888 (t80) REVERT: B 674 MET cc_start: 0.9361 (tpt) cc_final: 0.8907 (tpp) REVERT: B 677 MET cc_start: 0.9235 (tpp) cc_final: 0.8791 (tpp) REVERT: B 737 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8286 (pp) REVERT: B 764 MET cc_start: 0.8491 (mmm) cc_final: 0.8237 (mmm) REVERT: B 766 TYR cc_start: 0.8634 (m-80) cc_final: 0.8418 (m-10) REVERT: B 818 GLU cc_start: 0.7755 (tt0) cc_final: 0.7072 (tm-30) REVERT: B 1121 LEU cc_start: 0.8373 (tt) cc_final: 0.7978 (mp) REVERT: B 1130 THR cc_start: 0.5866 (OUTLIER) cc_final: 0.5592 (p) REVERT: C 59 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8416 (mp) REVERT: C 260 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8353 (tm-30) REVERT: D 39 MET cc_start: 0.9142 (tmm) cc_final: 0.8831 (tmm) REVERT: D 40 LEU cc_start: 0.9172 (mt) cc_final: 0.8786 (mt) REVERT: D 44 ARG cc_start: 0.9195 (tpp-160) cc_final: 0.8541 (tpp-160) REVERT: D 112 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7492 (mmtt) REVERT: E 18 MET cc_start: 0.8706 (mtt) cc_final: 0.8412 (mtm) REVERT: E 31 ASP cc_start: 0.9138 (p0) cc_final: 0.8934 (p0) REVERT: E 34 ASP cc_start: 0.8894 (m-30) cc_final: 0.8621 (p0) REVERT: E 72 MET cc_start: 0.7778 (ttp) cc_final: 0.7367 (ttp) REVERT: E 73 PHE cc_start: 0.7879 (t80) cc_final: 0.7195 (t80) REVERT: E 108 GLN cc_start: 0.8037 (tp40) cc_final: 0.7603 (tp-100) REVERT: E 133 GLN cc_start: 0.9228 (mp10) cc_final: 0.8995 (pm20) REVERT: E 138 ASN cc_start: 0.8695 (t0) cc_final: 0.8028 (p0) REVERT: E 192 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8462 (ptmm) REVERT: F 61 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8128 (mt-10) REVERT: G 3 TYR cc_start: 0.8543 (m-80) cc_final: 0.7991 (m-10) REVERT: G 24 ASN cc_start: 0.9108 (t0) cc_final: 0.8684 (t0) REVERT: G 33 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8261 (tm-30) REVERT: G 60 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6828 (tm-30) REVERT: G 164 MET cc_start: 0.8859 (mtt) cc_final: 0.8426 (mmt) REVERT: H 13 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8498 (mmtm) REVERT: H 20 LYS cc_start: 0.3166 (pttt) cc_final: 0.2653 (ttpp) REVERT: H 33 GLU cc_start: 0.8876 (pm20) cc_final: 0.8546 (pm20) REVERT: H 35 PHE cc_start: 0.8729 (m-10) cc_final: 0.8194 (m-10) REVERT: H 36 LYS cc_start: 0.7843 (pttm) cc_final: 0.6673 (tptt) REVERT: H 37 MET cc_start: 0.7197 (mpp) cc_final: 0.6320 (mmt) REVERT: H 66 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7261 (tp30) REVERT: H 95 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8192 (ttmm) REVERT: I 1 MET cc_start: 0.0181 (mtt) cc_final: -0.0973 (mtt) REVERT: I 24 LEU cc_start: 0.5918 (mp) cc_final: 0.5040 (mp) REVERT: I 41 ASN cc_start: 0.8281 (p0) cc_final: 0.7356 (p0) REVERT: J 19 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6881 (tm-30) REVERT: J 48 MET cc_start: 0.9060 (tpp) cc_final: 0.8330 (tpp) REVERT: J 62 TYR cc_start: 0.8498 (m-80) cc_final: 0.8020 (m-80) REVERT: K 68 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7897 (mm-30) REVERT: K 110 LYS cc_start: 0.8451 (tptp) cc_final: 0.8127 (tptp) REVERT: M 112 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7517 (mmt-90) REVERT: M 116 ASN cc_start: 0.8617 (m-40) cc_final: 0.7981 (m110) REVERT: M 139 ASN cc_start: 0.9343 (m-40) cc_final: 0.8996 (m110) REVERT: M 154 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7253 (mpt180) REVERT: M 181 CYS cc_start: 0.8696 (t) cc_final: 0.8472 (t) REVERT: M 193 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8855 (ttm170) REVERT: M 229 GLN cc_start: 0.9566 (tp40) cc_final: 0.9300 (tp40) REVERT: M 258 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9078 (mm) REVERT: M 300 PHE cc_start: 0.7807 (m-80) cc_final: 0.7336 (t80) REVERT: N 38 VAL cc_start: 0.6709 (p) cc_final: 0.6495 (m) REVERT: N 51 MET cc_start: 0.8148 (mmm) cc_final: 0.7718 (mmm) REVERT: N 339 TYR cc_start: 0.8947 (p90) cc_final: 0.8446 (p90) REVERT: N 344 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8015 (tmm160) REVERT: N 348 LYS cc_start: 0.9567 (mmmt) cc_final: 0.9323 (mmmt) REVERT: N 349 TRP cc_start: 0.8505 (m-90) cc_final: 0.8179 (m-90) REVERT: N 363 ARG cc_start: 0.9018 (mtm-85) cc_final: 0.8759 (mtm-85) REVERT: O 27 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7795 (pp30) REVERT: O 57 ASN cc_start: 0.9110 (m110) cc_final: 0.8333 (t0) REVERT: O 67 PHE cc_start: 0.8965 (t80) cc_final: 0.8337 (t80) REVERT: P 189 ASN cc_start: 0.7500 (t0) cc_final: 0.6817 (t0) REVERT: P 288 PHE cc_start: 0.7678 (t80) cc_final: 0.7384 (t80) REVERT: P 325 PHE cc_start: 0.8583 (t80) cc_final: 0.8368 (t80) REVERT: Q 25 PHE cc_start: 0.8538 (t80) cc_final: 0.8099 (t80) REVERT: Q 26 TYR cc_start: 0.8617 (m-80) cc_final: 0.8067 (m-80) REVERT: Q 48 MET cc_start: 0.8183 (mmm) cc_final: 0.7901 (mmt) REVERT: Q 76 MET cc_start: 0.7136 (mmp) cc_final: 0.6141 (tpt) REVERT: Q 93 PHE cc_start: 0.7706 (m-80) cc_final: 0.7254 (m-10) REVERT: Q 96 TYR cc_start: 0.8474 (m-80) cc_final: 0.8166 (m-80) REVERT: R 228 MET cc_start: 0.8213 (mmm) cc_final: 0.7335 (tpt) REVERT: S 14 TYR cc_start: 0.8710 (m-80) cc_final: 0.8321 (t80) REVERT: S 36 LYS cc_start: 0.9295 (mtmm) cc_final: 0.8610 (tptp) REVERT: S 96 GLN cc_start: 0.7114 (mp10) cc_final: 0.6528 (mp10) REVERT: S 110 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.6764 (t80) REVERT: S 136 GLU cc_start: 0.8164 (tp30) cc_final: 0.6932 (tp30) REVERT: S 168 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8333 (m-40) REVERT: S 173 HIS cc_start: 0.6879 (p90) cc_final: 0.6297 (m-70) REVERT: S 177 MET cc_start: 0.8102 (mmm) cc_final: 0.7169 (ttt) REVERT: T 56 PHE cc_start: 0.8013 (t80) cc_final: 0.7259 (t80) REVERT: T 153 TYR cc_start: 0.6663 (t80) cc_final: 0.6410 (t80) REVERT: T 186 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8746 (ttt) outliers start: 249 outliers final: 197 residues processed: 1226 average time/residue: 0.1775 time to fit residues: 361.2815 Evaluate side-chains 1261 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 1044 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 602 CYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 606 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1391 SER Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1445 HIS Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1058 LYS Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1161 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 154 ARG Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 193 ARG Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 258 ILE Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 312 GLU Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 344 ARG Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 365 TYR Chi-restraints excluded: chain O residue 63 ASN Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 71 PHE Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 198 ASN Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 29 MET Chi-restraints excluded: chain S residue 110 PHE Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 168 ASN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 186 MET Chi-restraints excluded: chain T residue 198 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 354 optimal weight: 3.9990 chunk 241 optimal weight: 0.3980 chunk 172 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 217 optimal weight: 0.4980 chunk 216 optimal weight: 0.5980 chunk 274 optimal weight: 0.9980 chunk 391 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN B 631 GLN C 5 ASN D 47 GLN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 278 GLN ** S 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.149199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103339 restraints weight = 103009.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099772 restraints weight = 75222.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100812 restraints weight = 60743.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101787 restraints weight = 48526.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101938 restraints weight = 43349.179| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 47913 Z= 0.171 Angle : 0.873 34.330 65405 Z= 0.444 Chirality : 0.048 0.482 7284 Planarity : 0.006 0.216 7920 Dihedral : 17.943 177.291 7716 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.77 % Favored : 91.67 % Rotamer: Outliers : 3.93 % Allowed : 25.23 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.92 (0.12), residues: 5357 helix: 0.51 (0.12), residues: 1934 sheet: -0.49 (0.19), residues: 762 loop : -1.51 (0.12), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 187 TYR 0.035 0.002 TYR G 167 PHE 0.075 0.002 PHE D 74 TRP 0.072 0.002 TRP T 31 HIS 0.016 0.001 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00389 (47907) covalent geometry : angle 0.87296 (65405) hydrogen bonds : bond 0.04562 ( 2010) hydrogen bonds : angle 5.34558 ( 5613) metal coordination : bond 0.00179 ( 5) Misc. bond : bond 0.00053 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10714 Ramachandran restraints generated. 5357 Oldfield, 0 Emsley, 5357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1109 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.7932 (ttm-80) REVERT: A 143 HIS cc_start: 0.9337 (m-70) cc_final: 0.9074 (m170) REVERT: A 212 LYS cc_start: 0.6354 (mmtp) cc_final: 0.5475 (mmtp) REVERT: A 233 CYS cc_start: 0.8881 (m) cc_final: 0.8345 (t) REVERT: A 242 TYR cc_start: 0.8697 (m-80) cc_final: 0.8319 (m-80) REVERT: A 266 MET cc_start: 0.6836 (tpp) cc_final: 0.6340 (tpp) REVERT: A 282 ASP cc_start: 0.8845 (m-30) cc_final: 0.8298 (t70) REVERT: A 321 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 341 GLN cc_start: 0.8813 (mm110) cc_final: 0.8553 (mm-40) REVERT: A 441 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: A 447 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: A 683 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 733 LEU cc_start: 0.9207 (mm) cc_final: 0.8914 (mm) REVERT: A 742 ASN cc_start: 0.8736 (t0) cc_final: 0.8063 (m-40) REVERT: A 749 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8690 (tmm-80) REVERT: A 955 GLU cc_start: 0.8452 (tp30) cc_final: 0.7840 (tp30) REVERT: A 959 MET cc_start: 0.8065 (mtt) cc_final: 0.7478 (mtt) REVERT: A 1004 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 1086 MET cc_start: 0.9205 (mmm) cc_final: 0.8673 (tpp) REVERT: A 1094 SER cc_start: 0.9059 (m) cc_final: 0.8732 (p) REVERT: A 1262 MET cc_start: 0.6480 (tpp) cc_final: 0.4739 (tpp) REVERT: A 1269 MET cc_start: 0.8275 (pmm) cc_final: 0.7977 (pmm) REVERT: A 1320 ILE cc_start: 0.9111 (mm) cc_final: 0.8703 (tp) REVERT: A 1332 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7910 (tp40) REVERT: A 1412 MET cc_start: 0.8361 (ttp) cc_final: 0.7754 (ppp) REVERT: A 1441 GLU cc_start: 0.7984 (tp30) cc_final: 0.7624 (tp30) REVERT: A 1463 LEU cc_start: 0.8240 (tp) cc_final: 0.8029 (mp) REVERT: A 1476 ASP cc_start: 0.8461 (t0) cc_final: 0.8171 (t0) REVERT: B 45 ASP cc_start: 0.8405 (m-30) cc_final: 0.8086 (m-30) REVERT: B 87 LYS cc_start: 0.8354 (tttm) cc_final: 0.8100 (ttmm) REVERT: B 130 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8705 (tttt) REVERT: B 144 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5686 (p-80) REVERT: B 176 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7586 (mm-30) REVERT: B 264 LYS cc_start: 0.8060 (mttm) cc_final: 0.7780 (mttm) REVERT: B 324 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7935 (mmm160) REVERT: B 363 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8540 (t80) REVERT: B 373 LEU cc_start: 0.9582 (mt) cc_final: 0.9250 (mm) REVERT: B 388 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: B 405 ARG cc_start: 0.8122 (ttm170) cc_final: 0.7526 (ttp-170) REVERT: B 422 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7886 (t80) REVERT: B 475 PHE cc_start: 0.8963 (t80) cc_final: 0.8586 (t80) REVERT: B 594 MET cc_start: 0.7478 (tmm) cc_final: 0.7261 (tmm) REVERT: B 677 MET cc_start: 0.9238 (tpp) cc_final: 0.8746 (tpp) REVERT: B 737 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8282 (pp) REVERT: B 764 MET cc_start: 0.8532 (mmm) cc_final: 0.8276 (mmm) REVERT: B 766 TYR cc_start: 0.8626 (m-80) cc_final: 0.8274 (m-10) REVERT: B 818 GLU cc_start: 0.7606 (tt0) cc_final: 0.7195 (tm-30) REVERT: B 1022 LEU cc_start: 0.8745 (pt) cc_final: 0.8416 (tt) REVERT: B 1121 LEU cc_start: 0.8356 (tt) cc_final: 0.7986 (mp) REVERT: B 1130 THR cc_start: 0.5725 (OUTLIER) cc_final: 0.5382 (p) REVERT: C 59 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8285 (mp) REVERT: C 260 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8240 (tm-30) REVERT: D 39 MET cc_start: 0.8947 (tmm) cc_final: 0.8601 (tmm) REVERT: D 40 LEU cc_start: 0.9092 (mt) cc_final: 0.8691 (mt) REVERT: D 44 ARG cc_start: 0.9048 (tpp-160) cc_final: 0.8492 (tpp-160) REVERT: E 8 TYR cc_start: 0.8610 (t80) cc_final: 0.8285 (t80) REVERT: E 18 MET cc_start: 0.8575 (mtt) cc_final: 0.8104 (ttm) REVERT: E 34 ASP cc_start: 0.8869 (m-30) cc_final: 0.8645 (p0) REVERT: E 72 MET cc_start: 0.7768 (ttp) cc_final: 0.7377 (ttp) REVERT: E 73 PHE cc_start: 0.7685 (t80) cc_final: 0.7152 (t80) REVERT: E 75 PHE cc_start: 0.8007 (t80) cc_final: 0.7516 (t80) REVERT: E 108 GLN cc_start: 0.8020 (tp40) cc_final: 0.7596 (tp-100) REVERT: E 138 ASN cc_start: 0.8610 (t0) cc_final: 0.7985 (p0) REVERT: F 61 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8038 (mt-10) REVERT: F 122 GLU cc_start: 0.8076 (mp0) cc_final: 0.7778 (mp0) REVERT: G 3 TYR cc_start: 0.8371 (m-80) cc_final: 0.8061 (m-10) REVERT: G 21 ASN cc_start: 0.8156 (p0) cc_final: 0.7726 (t0) REVERT: G 24 ASN cc_start: 0.8989 (t0) cc_final: 0.8636 (t0) REVERT: G 33 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8266 (tm-30) REVERT: G 60 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7031 (tm-30) REVERT: G 164 MET cc_start: 0.8494 (mtt) cc_final: 0.8177 (mmt) REVERT: H 21 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7825 (tmtt) REVERT: H 33 GLU cc_start: 0.8905 (pm20) cc_final: 0.8593 (pm20) REVERT: H 35 PHE cc_start: 0.8777 (m-10) cc_final: 0.8284 (m-10) REVERT: H 37 MET cc_start: 0.7246 (mpp) cc_final: 0.6942 (mmt) REVERT: H 66 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7571 (tp30) REVERT: H 95 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8100 (ttmm) REVERT: I 1 MET cc_start: -0.0653 (mtt) cc_final: -0.1673 (mtt) REVERT: I 24 LEU cc_start: 0.5654 (mp) cc_final: 0.4757 (mp) REVERT: I 41 ASN cc_start: 0.8207 (p0) cc_final: 0.7789 (p0) REVERT: I 74 GLN cc_start: 0.8312 (mp10) cc_final: 0.7827 (mp10) REVERT: I 108 MET cc_start: 0.8603 (mmm) cc_final: 0.8296 (mmp) REVERT: J 48 MET cc_start: 0.9005 (tpp) cc_final: 0.8281 (tpp) REVERT: J 62 TYR cc_start: 0.8430 (m-80) cc_final: 0.7936 (m-80) REVERT: K 68 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7848 (mm-30) REVERT: K 97 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8215 (mm-30) REVERT: L 29 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7553 (ttpt) REVERT: M 112 ARG cc_start: 0.8161 (tpp-160) cc_final: 0.7602 (mmt-90) REVERT: M 116 ASN cc_start: 0.8680 (m-40) cc_final: 0.8061 (m110) REVERT: M 139 ASN cc_start: 0.9347 (m-40) cc_final: 0.9009 (m110) REVERT: M 148 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7279 (tm-30) REVERT: M 154 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7218 (mpt180) REVERT: M 193 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8836 (ttm170) REVERT: M 229 GLN cc_start: 0.9501 (tp40) cc_final: 0.9272 (tp40) REVERT: M 258 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9032 (mm) REVERT: M 300 PHE cc_start: 0.7716 (m-80) cc_final: 0.7248 (t80) REVERT: N 51 MET cc_start: 0.8201 (mmm) cc_final: 0.7775 (mmm) REVERT: N 339 TYR cc_start: 0.8625 (p90) cc_final: 0.8185 (p90) REVERT: N 344 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7706 (tmm160) REVERT: N 348 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9233 (mmmt) REVERT: N 349 TRP cc_start: 0.8259 (m-90) cc_final: 0.8031 (m-90) REVERT: N 363 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8356 (ptt90) REVERT: O 27 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7422 (pp30) REVERT: O 57 ASN cc_start: 0.9103 (m110) cc_final: 0.8813 (t0) REVERT: O 67 PHE cc_start: 0.8860 (t80) cc_final: 0.8378 (t80) REVERT: P 189 ASN cc_start: 0.6898 (t0) cc_final: 0.6219 (t0) REVERT: P 278 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8524 (pm20) REVERT: P 325 PHE cc_start: 0.8341 (t80) cc_final: 0.8133 (t80) REVERT: Q 25 PHE cc_start: 0.8326 (t80) cc_final: 0.7981 (t80) REVERT: Q 26 TYR cc_start: 0.8122 (m-80) cc_final: 0.7694 (m-80) REVERT: Q 48 MET cc_start: 0.8150 (mmm) cc_final: 0.7897 (mmt) REVERT: Q 58 GLN cc_start: 0.8639 (pt0) cc_final: 0.8292 (pm20) REVERT: Q 60 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8037 (ttp80) REVERT: Q 76 MET cc_start: 0.6847 (mmp) cc_final: 0.5997 (tpt) REVERT: Q 93 PHE cc_start: 0.7675 (m-80) cc_final: 0.7248 (m-10) REVERT: R 228 MET cc_start: 0.8006 (mmm) cc_final: 0.7118 (tpt) REVERT: S 36 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8487 (tptp) REVERT: S 39 PHE cc_start: 0.8516 (m-10) cc_final: 0.8224 (m-10) REVERT: S 96 GLN cc_start: 0.7045 (mp10) cc_final: 0.6494 (mp10) REVERT: S 110 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7436 (t80) REVERT: S 136 GLU cc_start: 0.7721 (tp30) cc_final: 0.6468 (tp30) REVERT: S 173 HIS cc_start: 0.6814 (p90) cc_final: 0.5785 (m-70) REVERT: T 56 PHE cc_start: 0.7648 (t80) cc_final: 0.7131 (t80) REVERT: T 186 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8551 (ttt) outliers start: 188 outliers final: 153 residues processed: 1208 average time/residue: 0.1820 time to fit residues: 364.1194 Evaluate side-chains 1226 residues out of total 4784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1053 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1391 SER Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1445 HIS Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 631 GLN Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1058 LYS Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1092 ASP Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1161 GLU Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 154 ARG Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 193 ARG Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 258 ILE Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 312 GLU Chi-restraints excluded: chain N residue 314 LEU Chi-restraints excluded: chain N residue 344 ARG Chi-restraints excluded: chain N residue 351 PHE Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 365 TYR Chi-restraints excluded: chain O residue 63 ASN Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain P residue 165 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 278 GLN Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 14 LEU Chi-restraints excluded: chain Q residue 71 PHE Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 188 TYR Chi-restraints excluded: chain Q residue 198 ASN Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 29 MET Chi-restraints excluded: chain S residue 110 PHE Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 186 MET Chi-restraints excluded: chain T residue 198 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 158 optimal weight: 0.0020 chunk 74 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 346 optimal weight: 0.4980 chunk 5 optimal weight: 0.1980 chunk 340 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 545 optimal weight: 6.9990 chunk 542 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 162 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 = 0.4066 r_free = 0.4066 target = 0.149263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103960 restraints weight = 102639.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099398 restraints weight = 74271.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100812 restraints weight = 61372.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101743 restraints weight = 47638.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.101900 restraints weight = 42738.852| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.402 47913 Z= 0.287 Angle : 1.047 59.200 65405 Z= 0.583 Chirality : 0.054 1.704 7284 Planarity : 0.006 0.184 7920 Dihedral : 17.942 177.288 7716 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.95 % Favored : 91.49 % Rotamer: Outliers : 3.95 % Allowed : 25.67 % Favored : 70.38 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.91 (0.12), residues: 5357 helix: 0.53 (0.12), residues: 1921 sheet: -0.49 (0.19), residues: 762 loop : -1.50 (0.12), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.001 ARG L 42 TYR 0.065 0.002 TYR S 14 PHE 0.054 0.002 PHE D 74 TRP 0.069 0.002 TRP T 31 HIS 0.020 0.001 HIS B1117 Details of bonding type rmsd covalent geometry : bond 0.00633 (47907) covalent geometry : angle 1.04668 (65405) hydrogen bonds : bond 0.04583 ( 2010) hydrogen bonds : angle 5.35939 ( 5613) metal coordination : bond 0.00206 ( 5) Misc. bond : bond 0.00057 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9447.87 seconds wall clock time: 162 minutes 57.30 seconds (9777.30 seconds total)