Starting phenix.real_space_refine on Tue Aug 26 22:39:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrj_38604/08_2025/8xrj_38604.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrj_38604/08_2025/8xrj_38604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xrj_38604/08_2025/8xrj_38604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrj_38604/08_2025/8xrj_38604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xrj_38604/08_2025/8xrj_38604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrj_38604/08_2025/8xrj_38604.map" } resolution = 3.6 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= 0.001 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 8 6.06 5 P 315 5.49 5 Mg 1 5.21 5 S 208 5.16 5 C 26196 2.51 5 N 7684 2.21 5 O 8670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 43082 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 11173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11173 Classifications: {'peptide': 1410} Link IDs: {'PTRANS': 69, 'TRANS': 1340} Chain breaks: 4 Chain: "B" Number of atoms: 8932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8932 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 53, 'TRANS': 1061} Chain breaks: 5 Chain: "C" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2039 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 15, 'TRANS': 238} Chain breaks: 1 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "G" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1329 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 159} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "N" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain breaks: 1 Chain: "P" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 3233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3233 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Chain: "a" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "b" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "c" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "d" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "e" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "f" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "g" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "h" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 69.315 118.647 112.204 1.00 80.46 S ATOM 486 SG CYS A 74 66.042 116.879 112.188 1.00 81.07 S ATOM 533 SG CYS A 81 69.064 115.418 110.446 1.00 69.06 S ATOM 768 SG CYS A 111 55.931 126.903 64.806 1.00148.45 S ATOM 796 SG CYS A 114 53.699 128.715 66.703 1.00146.00 S ATOM 1142 SG CYS A 184 55.974 130.000 62.993 1.00174.54 S ATOM 19675 SG CYS B1119 52.809 116.557 102.522 1.00 88.67 S ATOM 19697 SG CYS B1122 55.427 116.900 99.740 1.00 85.06 S ATOM 19812 SG CYS B1137 55.385 119.184 102.778 1.00103.79 S ATOM 19833 SG CYS B1140 52.861 119.616 100.034 1.00107.41 S ATOM 20800 SG CYS C 88 99.472 65.375 145.378 1.00121.43 S ATOM 20813 SG CYS C 90 100.475 68.734 145.864 1.00137.60 S ATOM 20848 SG CYS C 94 103.201 66.566 146.461 1.00 97.20 S ATOM 20870 SG CYS C 97 101.790 66.777 142.822 1.00 95.16 S ATOM 28061 SG CYS I 17 106.153 105.167 26.078 1.00192.30 S ATOM 28085 SG CYS I 20 106.198 107.332 29.088 1.00193.64 S ATOM 28246 SG CYS I 39 102.858 106.293 28.441 1.00199.29 S ATOM 28271 SG CYS I 42 104.457 108.293 25.832 1.00197.45 S ATOM 28623 SG CYS I 86 115.607 63.116 37.792 1.00166.18 S ATOM 28647 SG CYS I 89 119.123 62.271 38.422 1.00175.05 S ATOM 28851 SG CYS I 114 117.411 63.912 41.284 1.00144.12 S ATOM 28886 SG CYS I 119 118.802 65.627 38.177 1.00161.27 S ATOM 28996 SG CYS J 7 108.443 56.055 113.545 1.00 47.29 S ATOM 29020 SG CYS J 10 107.866 53.094 115.826 1.00 46.75 S ATOM 29284 SG CYS J 44 107.605 52.597 111.983 1.00 49.79 S ATOM 29290 SG CYS J 45 110.738 52.818 114.000 1.00 51.83 S ATOM 30427 SG CYS L 19 124.458 97.447 118.068 1.00138.18 S ATOM 30446 SG CYS L 22 127.827 96.383 119.536 1.00150.40 S ATOM 30563 SG CYS L 36 126.202 99.761 120.505 1.00135.68 S ATOM 30589 SG CYS L 39 127.635 99.236 117.110 1.00138.32 S Time building chain proxies: 8.84, per 1000 atoms: 0.21 Number of scatterers: 43082 At special positions: 0 Unit cell: (160.06, 206.7, 204.58, 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 8 29.99 S 208 16.00 P 315 15.00 Mg 1 11.99 O 8670 8.00 N 7684 7.00 C 26196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " Number of angles added : 39 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8626 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 56 sheets defined 44.9% alpha, 16.6% beta 145 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 5.31 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 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.765A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.675A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 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 488 through 493 removed outlier: 3.641A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.581A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.672A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 3.599A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) 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: 3.637A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.713A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.533A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (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 927 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.809A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.110A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1019 removed outlier: 3.640A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1049 removed outlier: 5.257A pdb=" N LEU A1040 " --> pdb=" O ASN A1036 " (cutoff:3.500A) removed outlier: 5.653A 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 1079 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 4.078A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.015A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.655A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.142A 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 1189 through 1198 removed outlier: 4.671A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (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 1280 through 1296 removed outlier: 3.886A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.508A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 removed outlier: 3.508A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.986A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1421 Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.632A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.616A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.585A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1470 Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.560A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.660A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 4.674A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 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 308 removed outlier: 3.666A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.761A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 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 377 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 424 removed outlier: 4.056A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 516 through 520 removed outlier: 4.222A pdb=" N ALA B 519 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 520 " --> pdb=" O GLY B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 520' Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.802A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.540A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.650A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.032A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.688A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.797A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 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 124 through 128 removed outlier: 3.869A pdb=" N VAL C 127 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE C 128 " --> pdb=" O PRO C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 128' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 268 removed outlier: 3.790A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.810A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 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 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 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 17 through 27 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.954A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.992A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.058A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 77 removed outlier: 3.989A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.664A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 36 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.368A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 89 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 123 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.985A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.680A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.510A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 10.088A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.800A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.547A pdb=" N SER A 362 " --> pdb=" O ARG B1062 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.884A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.310A 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 602 through 605 removed outlier: 6.884A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB2, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.559A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 3.545A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB8, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.609A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.517A pdb=" N ALA B 196 " --> pdb=" O ARG B 484 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.705A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC5, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC6, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.037A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.514A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.514A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.673A pdb=" N VAL B 794 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N TYR B 949 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N MET B 796 " --> pdb=" O TYR B 949 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD3, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.904A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD5, first strand: chain 'B' and resid 1127 through 1128 Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.562A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.787A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.214A 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 'D' and resid 30 through 31 removed outlier: 7.207A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.819A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.513A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE5, first strand: chain 'G' and resid 84 through 93 removed outlier: 3.665A pdb=" N THR G 90 " --> pdb=" O PHE G 98 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.976A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.632A pdb=" N TYR I 25 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.609A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.901A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AF4, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AF5, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.210A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AF7, first strand: chain 'c' and resid 100 through 102 removed outlier: 6.401A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.807A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AG1, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.122A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'g' and resid 77 through 78 1777 hydrogen bonds defined for protein. 4971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 12.89 Time building geometry restraints manager: 3.99 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: 6828 1.32 - 1.44: 12792 1.44 - 1.57: 23943 1.57 - 1.70: 630 1.70 - 1.82: 330 Bond restraints: 44523 Sorted by residual: bond pdb=" CA HIS H 133 " pdb=" C HIS H 133 " ideal model delta sigma weight residual 1.522 1.574 -0.051 1.40e-02 5.10e+03 1.33e+01 bond pdb=" N PRO B 515 " pdb=" CD PRO B 515 " ideal model delta sigma weight residual 1.473 1.423 0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" CZ ARG B 242 " pdb=" NH2 ARG B 242 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" CD2 HIS A 301 " pdb=" NE2 HIS A 301 " ideal model delta sigma weight residual 1.374 1.337 0.037 1.10e-02 8.26e+03 1.14e+01 bond pdb=" CZ ARG B 491 " pdb=" NH2 ARG B 491 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.09e+01 ... (remaining 44518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 57703 2.09 - 4.19: 3421 4.19 - 6.28: 338 6.28 - 8.38: 38 8.38 - 10.47: 3 Bond angle restraints: 61503 Sorted by residual: angle pdb=" C GLN A 935 " pdb=" N GLU A 936 " pdb=" CA GLU A 936 " ideal model delta sigma weight residual 120.28 127.92 -7.64 1.34e+00 5.57e-01 3.25e+01 angle pdb=" N LYS D 91 " pdb=" CA LYS D 91 " pdb=" C LYS D 91 " ideal model delta sigma weight residual 110.24 117.96 -7.72 1.41e+00 5.03e-01 3.00e+01 angle pdb=" C GLU I 61 " pdb=" N VAL I 62 " pdb=" CA VAL I 62 " ideal model delta sigma weight residual 120.63 127.84 -7.21 1.33e+00 5.65e-01 2.94e+01 angle pdb=" C ARG B 230 " pdb=" N PRO B 231 " pdb=" CA PRO B 231 " ideal model delta sigma weight residual 119.89 125.40 -5.51 1.02e+00 9.61e-01 2.92e+01 angle pdb=" C LYS F 50 " pdb=" N ARG F 51 " pdb=" CA ARG F 51 " ideal model delta sigma weight residual 121.05 128.77 -7.72 1.43e+00 4.89e-01 2.92e+01 ... (remaining 61498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 24575 33.07 - 66.15: 1721 66.15 - 99.22: 84 99.22 - 132.29: 2 132.29 - 165.37: 3 Dihedral angle restraints: 26385 sinusoidal: 13044 harmonic: 13341 Sorted by residual: dihedral pdb=" CA ALA D 29 " pdb=" C ALA D 29 " pdb=" N GLU D 30 " pdb=" CA GLU D 30 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PHE G 98 " pdb=" C PHE G 98 " pdb=" N THR G 99 " pdb=" CA THR G 99 " ideal model delta harmonic sigma weight residual 180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA PRO B 832 " pdb=" C PRO B 832 " pdb=" N THR B 833 " pdb=" CA THR B 833 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 26382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 6383 0.105 - 0.210: 486 0.210 - 0.315: 46 0.315 - 0.420: 4 0.420 - 0.525: 5 Chirality restraints: 6924 Sorted by residual: chirality pdb=" P DA T 35 " pdb=" OP1 DA T 35 " pdb=" OP2 DA T 35 " pdb=" O5' DA T 35 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" P DC T 36 " pdb=" OP1 DC T 36 " pdb=" OP2 DC T 36 " pdb=" O5' DC T 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" P DT N 78 " pdb=" OP1 DT N 78 " pdb=" OP2 DT N 78 " pdb=" O5' DT N 78 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 6921 not shown) Planarity restraints: 6824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " 0.102 2.00e-02 2.50e+03 5.20e-02 6.76e+01 pdb=" CG TRP B 99 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " -0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " -0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 46 " -0.061 2.00e-02 2.50e+03 4.65e-02 6.50e+01 pdb=" N9 DG N 46 " 0.031 2.00e-02 2.50e+03 pdb=" C8 DG N 46 " -0.033 2.00e-02 2.50e+03 pdb=" N7 DG N 46 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG N 46 " 0.029 2.00e-02 2.50e+03 pdb=" C6 DG N 46 " 0.008 2.00e-02 2.50e+03 pdb=" O6 DG N 46 " -0.057 2.00e-02 2.50e+03 pdb=" N1 DG N 46 " 0.036 2.00e-02 2.50e+03 pdb=" C2 DG N 46 " 0.039 2.00e-02 2.50e+03 pdb=" N2 DG N 46 " -0.089 2.00e-02 2.50e+03 pdb=" N3 DG N 46 " 0.050 2.00e-02 2.50e+03 pdb=" C4 DG N 46 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 74 " 0.081 2.00e-02 2.50e+03 5.16e-02 4.66e+01 pdb=" CG PHE D 74 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE D 74 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE D 74 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE D 74 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE D 74 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 74 " 0.062 2.00e-02 2.50e+03 ... (remaining 6821 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 138 2.56 - 3.15: 32887 3.15 - 3.73: 68479 3.73 - 4.32: 97229 4.32 - 4.90: 155488 Nonbonded interactions: 354221 Sorted by model distance: nonbonded pdb=" OP1 U P 11 " pdb="MG MG A2003 " model vdw 1.977 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 2.011 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 2.064 2.170 nonbonded pdb=" O3' C P 10 " pdb="MG MG A2003 " model vdw 2.098 2.170 nonbonded pdb=" OH TYR B 215 " pdb=" OE2 GLU B 266 " model vdw 2.209 3.040 ... (remaining 354216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = (chain 'b' and resid 25 through 101) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 16 through 117) selection = chain 'g' } ncs_group { reference = chain 'd' selection = (chain 'h' and resid 33 through 124) } 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 46.900 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.090 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.158 44554 Z= 0.362 Angle : 1.017 20.032 61542 Z= 0.634 Chirality : 0.061 0.525 6924 Planarity : 0.010 0.127 6824 Dihedral : 18.898 165.366 17759 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.02 % Allowed : 6.83 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.12), residues: 4528 helix: 0.64 (0.12), residues: 1864 sheet: 0.14 (0.21), residues: 547 loop : -0.35 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A1052 TYR 0.085 0.005 TYR G 17 PHE 0.081 0.005 PHE D 74 TRP 0.102 0.005 TRP B 99 HIS 0.013 0.002 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00632 (44523) covalent geometry : angle 1.00080 (61503) hydrogen bonds : bond 0.12751 ( 2111) hydrogen bonds : angle 5.72383 ( 5705) metal coordination : bond 0.04469 ( 31) metal coordination : angle 7.26124 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 421 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.8803 (tp) cc_final: 0.8566 (tp) REVERT: A 524 MET cc_start: 0.7662 (mmp) cc_final: 0.7078 (mtp) REVERT: A 561 MET cc_start: 0.8069 (mtt) cc_final: 0.7514 (mmt) REVERT: A 565 MET cc_start: 0.8779 (tpt) cc_final: 0.8552 (tpp) REVERT: A 1054 MET cc_start: 0.8307 (tpp) cc_final: 0.8006 (mmm) REVERT: A 1226 LEU cc_start: 0.8473 (mt) cc_final: 0.8208 (mp) REVERT: B 1131 ARG cc_start: 0.7363 (mtt180) cc_final: 0.6385 (ptp-170) REVERT: B 1172 MET cc_start: 0.8305 (mmm) cc_final: 0.8064 (mmt) REVERT: C 214 ASP cc_start: 0.7640 (m-30) cc_final: 0.7345 (p0) REVERT: F 126 THR cc_start: 0.7365 (p) cc_final: 0.6863 (t) REVERT: H 65 TYR cc_start: 0.7049 (m-80) cc_final: 0.6848 (m-10) REVERT: I 91 HIS cc_start: 0.7416 (m170) cc_final: 0.7191 (m90) REVERT: L 43 ILE cc_start: 0.8514 (mt) cc_final: 0.7427 (mm) REVERT: d 59 MET cc_start: 0.0323 (tpt) cc_final: -0.0013 (ttp) REVERT: f 45 ARG cc_start: -0.1073 (ttt-90) cc_final: -0.2024 (mpt-90) REVERT: h 108 LYS cc_start: 0.6617 (mptt) cc_final: 0.6345 (mttp) outliers start: 1 outliers final: 1 residues processed: 422 average time/residue: 0.2967 time to fit residues: 199.6354 Evaluate side-chains 204 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 0.1980 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS A 671 ASN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN B 582 GLN C 51 GLN C 217 GLN C 260 GLN C 265 HIS I 45 GLN a 108 ASN ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 112 GLN h 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.091534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.067962 restraints weight = 208332.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.066172 restraints weight = 167386.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.066682 restraints weight = 191303.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.066336 restraints weight = 151487.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.066544 restraints weight = 130744.319| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44554 Z= 0.170 Angle : 0.639 20.046 61542 Z= 0.342 Chirality : 0.043 0.194 6924 Planarity : 0.004 0.051 6824 Dihedral : 21.931 161.315 8546 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.15 % Allowed : 8.70 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.12), residues: 4528 helix: 1.54 (0.12), residues: 1869 sheet: 0.08 (0.21), residues: 594 loop : -0.17 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG h 86 TYR 0.024 0.002 TYR L 41 PHE 0.023 0.002 PHE G 44 TRP 0.036 0.002 TRP A1192 HIS 0.013 0.001 HIS L 23 Details of bonding type rmsd covalent geometry : bond 0.00379 (44523) covalent geometry : angle 0.61746 (61503) hydrogen bonds : bond 0.04585 ( 2111) hydrogen bonds : angle 4.50145 ( 5705) metal coordination : bond 0.00799 ( 31) metal coordination : angle 6.57479 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3904 (OUTLIER) cc_final: 0.2845 (tpt) REVERT: A 484 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8418 (pp) REVERT: A 565 MET cc_start: 0.8965 (tpt) cc_final: 0.8676 (tpt) REVERT: A 1054 MET cc_start: 0.8304 (tpp) cc_final: 0.8008 (mmm) REVERT: A 1226 LEU cc_start: 0.8477 (mt) cc_final: 0.8248 (mt) REVERT: A 1239 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.5904 (t80) REVERT: B 550 MET cc_start: 0.7686 (tmm) cc_final: 0.7036 (tmm) REVERT: B 1172 MET cc_start: 0.8254 (mmm) cc_final: 0.8019 (mmt) REVERT: C 214 ASP cc_start: 0.8022 (m-30) cc_final: 0.7553 (p0) REVERT: D 45 LYS cc_start: 0.6988 (tptt) cc_final: 0.6368 (pttt) REVERT: D 67 TYR cc_start: 0.3278 (t80) cc_final: 0.2887 (t80) REVERT: D 109 GLU cc_start: 0.4980 (tp30) cc_final: 0.4008 (pm20) REVERT: G 35 GLU cc_start: 0.5861 (mt-10) cc_final: 0.5548 (mm-30) REVERT: G 131 MET cc_start: 0.6020 (mmt) cc_final: 0.4929 (tpt) REVERT: I 91 HIS cc_start: 0.7602 (m170) cc_final: 0.7130 (m90) REVERT: d 59 MET cc_start: -0.0585 (tpt) cc_final: -0.1124 (tmm) REVERT: f 45 ARG cc_start: -0.1343 (ttt-90) cc_final: -0.2071 (mpt-90) REVERT: f 67 ARG cc_start: 0.4690 (tmt170) cc_final: 0.3934 (tpt90) REVERT: g 57 TYR cc_start: 0.4345 (t80) cc_final: 0.4092 (t80) outliers start: 46 outliers final: 17 residues processed: 248 average time/residue: 0.2260 time to fit residues: 94.5469 Evaluate side-chains 200 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1239 PHE Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain c residue 24 GLN Chi-restraints excluded: chain h residue 63 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 333 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 420 optimal weight: 9.9990 chunk 371 optimal weight: 0.0670 chunk 325 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 454 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS C 66 HIS D 38 HIS ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN e 108 ASN ** h 82 HIS ** 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 = 0.4233 r_free = 0.4233 target = 0.090149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.066596 restraints weight = 208878.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.064812 restraints weight = 165764.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.065206 restraints weight = 193609.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.065037 restraints weight = 145903.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.065165 restraints weight = 124344.328| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 44554 Z= 0.178 Angle : 0.607 15.146 61542 Z= 0.326 Chirality : 0.042 0.174 6924 Planarity : 0.004 0.053 6824 Dihedral : 21.780 163.446 8546 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.70 % Allowed : 8.65 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.12), residues: 4528 helix: 1.69 (0.12), residues: 1872 sheet: 0.00 (0.20), residues: 595 loop : -0.20 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1141 TYR 0.021 0.002 TYR a 54 PHE 0.022 0.002 PHE A 802 TRP 0.025 0.002 TRP A1192 HIS 0.020 0.001 HIS L 23 Details of bonding type rmsd covalent geometry : bond 0.00400 (44523) covalent geometry : angle 0.59019 (61503) hydrogen bonds : bond 0.04187 ( 2111) hydrogen bonds : angle 4.31292 ( 5705) metal coordination : bond 0.00913 ( 31) metal coordination : angle 5.60969 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.4012 (OUTLIER) cc_final: 0.3253 (tpt) REVERT: A 329 MET cc_start: 0.7304 (mmt) cc_final: 0.7031 (mmt) REVERT: A 484 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8482 (pp) REVERT: A 565 MET cc_start: 0.8986 (tpt) cc_final: 0.8720 (tpt) REVERT: A 1054 MET cc_start: 0.8330 (tpp) cc_final: 0.8022 (mmm) REVERT: A 1239 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.5372 (t80) REVERT: B 348 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 550 MET cc_start: 0.7713 (tmm) cc_final: 0.7049 (tmm) REVERT: B 1172 MET cc_start: 0.8305 (mmm) cc_final: 0.8097 (mmt) REVERT: C 211 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8187 (mt) REVERT: C 214 ASP cc_start: 0.8173 (m-30) cc_final: 0.7626 (p0) REVERT: D 45 LYS cc_start: 0.6677 (tptt) cc_final: 0.6088 (pttt) REVERT: D 67 TYR cc_start: 0.3180 (t80) cc_final: 0.2638 (t80) REVERT: G 28 GLN cc_start: 0.8153 (pt0) cc_final: 0.7730 (tm-30) REVERT: G 131 MET cc_start: 0.5886 (mmt) cc_final: 0.4938 (tpt) REVERT: I 91 HIS cc_start: 0.7513 (m170) cc_final: 0.6935 (m90) REVERT: d 59 MET cc_start: -0.0413 (tpt) cc_final: -0.1021 (tmm) REVERT: f 45 ARG cc_start: -0.1671 (ttt-90) cc_final: -0.2276 (mpt-90) outliers start: 68 outliers final: 23 residues processed: 248 average time/residue: 0.2217 time to fit residues: 94.3739 Evaluate side-chains 200 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1239 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 585 ASN Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain L residue 24 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 183 optimal weight: 4.9990 chunk 428 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 320 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 365 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 464 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 861 GLN A1093 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 HIS B 650 ASN B 731 GLN B1120 ASN C 5 ASN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 HIS ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 89 ASN ** g 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.087563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.064274 restraints weight = 209446.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.062443 restraints weight = 181345.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.062729 restraints weight = 221482.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.062489 restraints weight = 170110.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.062618 restraints weight = 140139.403| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 44554 Z= 0.393 Angle : 0.815 25.132 61542 Z= 0.426 Chirality : 0.049 0.255 6924 Planarity : 0.006 0.071 6824 Dihedral : 22.050 162.486 8543 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.17 % Allowed : 10.25 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.12), residues: 4528 helix: 0.80 (0.11), residues: 1859 sheet: -0.43 (0.20), residues: 601 loop : -0.65 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 73 TYR 0.031 0.003 TYR B 811 PHE 0.030 0.003 PHE C 63 TRP 0.027 0.003 TRP C 49 HIS 0.011 0.002 HIS L 23 Details of bonding type rmsd covalent geometry : bond 0.00916 (44523) covalent geometry : angle 0.79346 (61503) hydrogen bonds : bond 0.05756 ( 2111) hydrogen bonds : angle 4.83552 ( 5705) metal coordination : bond 0.01824 ( 31) metal coordination : angle 7.47039 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 172 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.7040 (OUTLIER) cc_final: 0.6753 (t-90) REVERT: A 264 VAL cc_start: 0.7901 (t) cc_final: 0.7554 (m) REVERT: A 266 MET cc_start: 0.3913 (OUTLIER) cc_final: 0.3307 (tpt) REVERT: A 329 MET cc_start: 0.7537 (mmt) cc_final: 0.7307 (mmt) REVERT: A 470 MET cc_start: 0.8810 (mtt) cc_final: 0.8416 (mtt) REVERT: A 484 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8554 (pp) REVERT: A 524 MET cc_start: 0.7982 (mmm) cc_final: 0.7700 (mtp) REVERT: A 1239 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.5815 (t80) REVERT: B 300 MET cc_start: 0.7707 (mmm) cc_final: 0.7322 (tpt) REVERT: B 550 MET cc_start: 0.7840 (tmm) cc_final: 0.7102 (tmm) REVERT: B 1048 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: B 1131 ARG cc_start: 0.7711 (mtt180) cc_final: 0.6971 (mmt90) REVERT: C 214 ASP cc_start: 0.8145 (m-30) cc_final: 0.7662 (p0) REVERT: D 45 LYS cc_start: 0.6455 (tptt) cc_final: 0.6016 (pttt) REVERT: G 21 ASN cc_start: 0.7639 (t0) cc_final: 0.7407 (t0) REVERT: G 131 MET cc_start: 0.5732 (mmt) cc_final: 0.4550 (tpp) REVERT: d 59 MET cc_start: 0.0121 (tpt) cc_final: -0.0371 (ttp) REVERT: f 45 ARG cc_start: -0.1219 (ttt-90) cc_final: -0.2028 (mmt-90) REVERT: h 62 MET cc_start: 0.1091 (OUTLIER) cc_final: 0.0687 (tmm) outliers start: 87 outliers final: 38 residues processed: 246 average time/residue: 0.2399 time to fit residues: 103.0675 Evaluate side-chains 210 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1239 PHE Chi-restraints excluded: chain A residue 1316 ASN Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 62 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 49 optimal weight: 1.9990 chunk 479 optimal weight: 9.9990 chunk 358 optimal weight: 20.0000 chunk 273 optimal weight: 0.0020 chunk 81 optimal weight: 0.9990 chunk 360 optimal weight: 0.8980 chunk 431 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.089668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.066052 restraints weight = 207163.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.064492 restraints weight = 166215.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.064641 restraints weight = 175232.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.064829 restraints weight = 125998.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.065006 restraints weight = 114119.023| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44554 Z= 0.123 Angle : 0.574 16.864 61542 Z= 0.307 Chirality : 0.041 0.164 6924 Planarity : 0.004 0.051 6824 Dihedral : 21.847 161.130 8543 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.65 % Allowed : 10.95 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.12), residues: 4528 helix: 1.52 (0.12), residues: 1867 sheet: -0.24 (0.20), residues: 585 loop : -0.35 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 138 TYR 0.030 0.001 TYR L 41 PHE 0.025 0.001 PHE G 44 TRP 0.031 0.002 TRP A1192 HIS 0.008 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00265 (44523) covalent geometry : angle 0.55742 (61503) hydrogen bonds : bond 0.03766 ( 2111) hydrogen bonds : angle 4.30568 ( 5705) metal coordination : bond 0.00582 ( 31) metal coordination : angle 5.43830 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 1.699 Fit side-chains revert: symmetry clash REVERT: A 264 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7705 (m) REVERT: A 329 MET cc_start: 0.7422 (mmt) cc_final: 0.7166 (mmt) REVERT: A 470 MET cc_start: 0.8791 (mtm) cc_final: 0.8577 (mtt) REVERT: A 581 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7958 (ttmt) REVERT: A 1239 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.5521 (t80) REVERT: A 1246 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6553 (tt) REVERT: B 300 MET cc_start: 0.7566 (mmm) cc_final: 0.7251 (tpt) REVERT: B 550 MET cc_start: 0.7752 (tmm) cc_final: 0.7002 (tmm) REVERT: C 214 ASP cc_start: 0.8100 (m-30) cc_final: 0.7706 (p0) REVERT: D 34 ASN cc_start: 0.2115 (OUTLIER) cc_final: 0.1470 (t0) REVERT: D 67 TYR cc_start: 0.3454 (t80) cc_final: 0.2837 (t80) REVERT: E 48 PRO cc_start: 0.7570 (Cg_endo) cc_final: 0.7287 (Cg_exo) REVERT: G 21 ASN cc_start: 0.7719 (t0) cc_final: 0.7506 (t0) REVERT: G 28 GLN cc_start: 0.8228 (pt0) cc_final: 0.7838 (tm-30) REVERT: G 131 MET cc_start: 0.5630 (mmt) cc_final: 0.4399 (tpp) REVERT: d 59 MET cc_start: -0.0020 (tpt) cc_final: -0.0412 (ttp) REVERT: f 45 ARG cc_start: -0.1502 (ttt-90) cc_final: -0.2141 (mpt-90) REVERT: h 62 MET cc_start: 0.0858 (OUTLIER) cc_final: 0.0561 (tmm) outliers start: 66 outliers final: 32 residues processed: 223 average time/residue: 0.2484 time to fit residues: 96.9469 Evaluate side-chains 204 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1239 PHE Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain e residue 62 ILE Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain h residue 62 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 449 optimal weight: 30.0000 chunk 312 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 370 optimal weight: 5.9990 chunk 475 optimal weight: 9.9990 chunk 431 optimal weight: 9.9990 chunk 318 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.088545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.064874 restraints weight = 208419.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.063119 restraints weight = 170580.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.063513 restraints weight = 198635.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.063214 restraints weight = 157045.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.063414 restraints weight = 133843.066| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 44554 Z= 0.206 Angle : 0.615 17.591 61542 Z= 0.327 Chirality : 0.042 0.181 6924 Planarity : 0.004 0.051 6824 Dihedral : 21.828 161.303 8543 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.00 % Allowed : 11.27 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.12), residues: 4528 helix: 1.47 (0.12), residues: 1865 sheet: -0.29 (0.21), residues: 589 loop : -0.43 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 98 TYR 0.026 0.002 TYR L 41 PHE 0.023 0.002 PHE G 44 TRP 0.028 0.002 TRP A1192 HIS 0.030 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00472 (44523) covalent geometry : angle 0.59912 (61503) hydrogen bonds : bond 0.04250 ( 2111) hydrogen bonds : angle 4.35649 ( 5705) metal coordination : bond 0.01055 ( 31) metal coordination : angle 5.57245 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 173 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6544 (OUTLIER) cc_final: 0.6019 (t-90) REVERT: A 329 MET cc_start: 0.7456 (mmt) cc_final: 0.7165 (mmt) REVERT: A 581 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7978 (ttmt) REVERT: A 1221 MET cc_start: 0.8278 (tmm) cc_final: 0.7857 (tmm) REVERT: A 1226 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8515 (pp) REVERT: A 1239 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.5724 (t80) REVERT: A 1246 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6539 (tt) REVERT: B 300 MET cc_start: 0.7570 (mmm) cc_final: 0.7267 (tpt) REVERT: B 550 MET cc_start: 0.7797 (tmm) cc_final: 0.6969 (tmm) REVERT: B 1048 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7404 (m-10) REVERT: C 179 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.9059 (m) REVERT: C 214 ASP cc_start: 0.8053 (m-30) cc_final: 0.7695 (p0) REVERT: D 34 ASN cc_start: 0.1898 (OUTLIER) cc_final: 0.1356 (t0) REVERT: D 67 TYR cc_start: 0.3643 (t80) cc_final: 0.3138 (t80) REVERT: G 21 ASN cc_start: 0.7683 (t0) cc_final: 0.7452 (t0) REVERT: G 28 GLN cc_start: 0.8196 (pt0) cc_final: 0.7755 (tm-30) REVERT: G 131 MET cc_start: 0.5588 (mmt) cc_final: 0.4354 (tpp) REVERT: K 34 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8544 (p) REVERT: d 59 MET cc_start: 0.0203 (tpt) cc_final: -0.0332 (ttp) REVERT: e 118 THR cc_start: 0.0734 (m) cc_final: -0.0895 (p) REVERT: f 45 ARG cc_start: -0.1480 (ttt-90) cc_final: -0.2094 (mmt-90) REVERT: h 62 MET cc_start: 0.0669 (OUTLIER) cc_final: 0.0359 (tmm) outliers start: 80 outliers final: 43 residues processed: 243 average time/residue: 0.2416 time to fit residues: 102.9239 Evaluate side-chains 217 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1239 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain e residue 62 ILE Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain h residue 62 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 324 optimal weight: 9.9990 chunk 448 optimal weight: 5.9990 chunk 321 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 462 optimal weight: 2.9990 chunk 357 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 450 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN a 113 HIS ** h 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.088318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.064614 restraints weight = 208541.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.062943 restraints weight = 166392.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.063348 restraints weight = 190714.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.063045 restraints weight = 154679.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.063274 restraints weight = 131714.411| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 44554 Z= 0.181 Angle : 0.589 17.132 61542 Z= 0.314 Chirality : 0.042 0.176 6924 Planarity : 0.004 0.049 6824 Dihedral : 21.804 161.471 8543 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.90 % Allowed : 11.57 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.12), residues: 4528 helix: 1.51 (0.12), residues: 1867 sheet: -0.41 (0.20), residues: 596 loop : -0.45 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 92 TYR 0.025 0.002 TYR L 41 PHE 0.023 0.002 PHE G 44 TRP 0.031 0.002 TRP A1192 HIS 0.010 0.001 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00414 (44523) covalent geometry : angle 0.57378 (61503) hydrogen bonds : bond 0.03911 ( 2111) hydrogen bonds : angle 4.30218 ( 5705) metal coordination : bond 0.00938 ( 31) metal coordination : angle 5.38008 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 170 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6397 (OUTLIER) cc_final: 0.5907 (t-90) REVERT: A 329 MET cc_start: 0.7432 (mmt) cc_final: 0.7137 (mmt) REVERT: A 1221 MET cc_start: 0.8375 (tmm) cc_final: 0.7909 (tmm) REVERT: A 1226 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8412 (pp) REVERT: A 1239 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.5795 (t80) REVERT: A 1246 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6507 (tt) REVERT: B 550 MET cc_start: 0.7776 (tmm) cc_final: 0.7001 (tmm) REVERT: C 66 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7771 (t70) REVERT: C 179 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9046 (m) REVERT: C 214 ASP cc_start: 0.8070 (m-30) cc_final: 0.7690 (p0) REVERT: D 34 ASN cc_start: 0.1899 (OUTLIER) cc_final: 0.1384 (t0) REVERT: D 67 TYR cc_start: 0.3904 (t80) cc_final: 0.3298 (t80) REVERT: G 28 GLN cc_start: 0.8207 (pt0) cc_final: 0.7761 (tm-30) REVERT: G 131 MET cc_start: 0.5548 (mmt) cc_final: 0.4153 (tmm) REVERT: K 34 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8466 (p) REVERT: d 59 MET cc_start: 0.0257 (tpt) cc_final: -0.0253 (ttp) REVERT: e 118 THR cc_start: 0.0874 (m) cc_final: -0.0757 (p) REVERT: f 45 ARG cc_start: -0.1422 (ttt-90) cc_final: -0.2040 (mmt-90) REVERT: h 62 MET cc_start: 0.0780 (OUTLIER) cc_final: 0.0474 (tmm) outliers start: 76 outliers final: 44 residues processed: 236 average time/residue: 0.2163 time to fit residues: 89.6203 Evaluate side-chains 218 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1239 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1316 ASN Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain e residue 62 ILE Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 42 TYR Chi-restraints excluded: chain h residue 62 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 82 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 298 optimal weight: 0.4980 chunk 202 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 97 optimal weight: 0.0000 chunk 317 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN C 157 GLN a 113 HIS ** h 82 HIS ** 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 = 0.4217 r_free = 0.4217 target = 0.089535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.065709 restraints weight = 209489.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.064326 restraints weight = 158953.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.064739 restraints weight = 172262.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.064562 restraints weight = 135560.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.064608 restraints weight = 114851.900| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44554 Z= 0.115 Angle : 0.549 12.182 61542 Z= 0.293 Chirality : 0.040 0.511 6924 Planarity : 0.004 0.051 6824 Dihedral : 21.668 160.916 8543 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.20 % Allowed : 12.54 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.13), residues: 4528 helix: 1.80 (0.12), residues: 1876 sheet: -0.25 (0.20), residues: 599 loop : -0.28 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 74 TYR 0.019 0.001 TYR a 54 PHE 0.018 0.001 PHE G 44 TRP 0.024 0.002 TRP C 49 HIS 0.007 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00250 (44523) covalent geometry : angle 0.53732 (61503) hydrogen bonds : bond 0.03330 ( 2111) hydrogen bonds : angle 4.08773 ( 5705) metal coordination : bond 0.00522 ( 31) metal coordination : angle 4.47465 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6232 (OUTLIER) cc_final: 0.5724 (t-90) REVERT: A 329 MET cc_start: 0.7466 (mmt) cc_final: 0.7140 (mmt) REVERT: A 1221 MET cc_start: 0.8361 (tmm) cc_final: 0.7882 (tmm) REVERT: A 1226 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8365 (pp) REVERT: A 1239 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.5769 (t80) REVERT: A 1412 MET cc_start: 0.8729 (ttp) cc_final: 0.8224 (tmm) REVERT: B 550 MET cc_start: 0.7789 (tmm) cc_final: 0.6998 (tmm) REVERT: C 214 ASP cc_start: 0.8141 (m-30) cc_final: 0.7770 (p0) REVERT: D 34 ASN cc_start: 0.2348 (OUTLIER) cc_final: 0.1939 (t0) REVERT: D 67 TYR cc_start: 0.4131 (t80) cc_final: 0.3663 (t80) REVERT: E 48 PRO cc_start: 0.7687 (Cg_endo) cc_final: 0.7469 (Cg_exo) REVERT: G 28 GLN cc_start: 0.8062 (pt0) cc_final: 0.7722 (tm-30) REVERT: G 35 GLU cc_start: 0.5868 (mt-10) cc_final: 0.5578 (mm-30) REVERT: G 131 MET cc_start: 0.5551 (mmt) cc_final: 0.4053 (tmm) REVERT: d 59 MET cc_start: 0.0183 (tpt) cc_final: -0.0487 (ttp) REVERT: e 118 THR cc_start: 0.0848 (m) cc_final: -0.0529 (p) REVERT: f 45 ARG cc_start: -0.1412 (ttt-90) cc_final: -0.2286 (mmt-90) REVERT: h 62 MET cc_start: 0.0565 (OUTLIER) cc_final: 0.0300 (tmm) outliers start: 48 outliers final: 33 residues processed: 217 average time/residue: 0.2185 time to fit residues: 83.2242 Evaluate side-chains 206 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1239 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain h residue 42 TYR Chi-restraints excluded: chain h residue 62 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 442 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 393 optimal weight: 10.0000 chunk 411 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.088679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.064224 restraints weight = 207619.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.063186 restraints weight = 156651.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.063304 restraints weight = 154321.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.063467 restraints weight = 118196.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.063509 restraints weight = 107504.991| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 44554 Z= 0.158 Angle : 0.570 14.618 61542 Z= 0.303 Chirality : 0.041 0.171 6924 Planarity : 0.004 0.050 6824 Dihedral : 21.670 161.691 8543 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.35 % Allowed : 12.59 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.13), residues: 4528 helix: 1.79 (0.12), residues: 1869 sheet: -0.20 (0.21), residues: 581 loop : -0.34 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.018 0.001 TYR L 41 PHE 0.018 0.001 PHE G 44 TRP 0.028 0.002 TRP A1192 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00358 (44523) covalent geometry : angle 0.55712 (61503) hydrogen bonds : bond 0.03744 ( 2111) hydrogen bonds : angle 4.13146 ( 5705) metal coordination : bond 0.00851 ( 31) metal coordination : angle 4.85947 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6313 (OUTLIER) cc_final: 0.5783 (t-90) REVERT: A 329 MET cc_start: 0.7411 (mmt) cc_final: 0.7096 (mmt) REVERT: A 1221 MET cc_start: 0.8409 (tmm) cc_final: 0.7948 (tmm) REVERT: A 1226 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8403 (pp) REVERT: A 1239 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5822 (t80) REVERT: A 1412 MET cc_start: 0.8696 (ttp) cc_final: 0.8290 (tmm) REVERT: B 550 MET cc_start: 0.7756 (tmm) cc_final: 0.6889 (tmm) REVERT: B 954 MET cc_start: 0.8263 (mtp) cc_final: 0.8037 (ttt) REVERT: C 66 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7837 (t70) REVERT: C 214 ASP cc_start: 0.8094 (m-30) cc_final: 0.7752 (p0) REVERT: D 34 ASN cc_start: 0.2371 (OUTLIER) cc_final: 0.1997 (t0) REVERT: D 67 TYR cc_start: 0.4095 (t80) cc_final: 0.3645 (t80) REVERT: G 28 GLN cc_start: 0.8061 (pt0) cc_final: 0.7744 (tm-30) REVERT: G 131 MET cc_start: 0.5624 (mmt) cc_final: 0.3980 (tmm) REVERT: K 34 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8486 (p) REVERT: d 59 MET cc_start: 0.0347 (tpt) cc_final: -0.0409 (ttp) REVERT: f 45 ARG cc_start: -0.1293 (ttt-90) cc_final: -0.2169 (mmt-90) REVERT: h 62 MET cc_start: 0.0534 (OUTLIER) cc_final: 0.0244 (tmm) outliers start: 54 outliers final: 36 residues processed: 214 average time/residue: 0.2470 time to fit residues: 91.9333 Evaluate side-chains 205 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1239 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain h residue 42 TYR Chi-restraints excluded: chain h residue 62 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 338 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 413 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 409 optimal weight: 30.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** h 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.088465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.064454 restraints weight = 207679.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.063757 restraints weight = 154423.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.063843 restraints weight = 168097.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.063898 restraints weight = 128862.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.063996 restraints weight = 110600.402| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 44554 Z= 0.163 Angle : 0.577 15.641 61542 Z= 0.306 Chirality : 0.041 0.183 6924 Planarity : 0.004 0.049 6824 Dihedral : 21.677 161.589 8543 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.20 % Allowed : 12.62 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.13), residues: 4528 helix: 1.75 (0.12), residues: 1866 sheet: -0.29 (0.21), residues: 586 loop : -0.39 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 74 TYR 0.015 0.001 TYR L 41 PHE 0.016 0.001 PHE G 44 TRP 0.024 0.002 TRP A1192 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00371 (44523) covalent geometry : angle 0.56344 (61503) hydrogen bonds : bond 0.03729 ( 2111) hydrogen bonds : angle 4.17896 ( 5705) metal coordination : bond 0.00878 ( 31) metal coordination : angle 4.90528 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9056 Ramachandran restraints generated. 4528 Oldfield, 0 Emsley, 4528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6240 (OUTLIER) cc_final: 0.5700 (t-90) REVERT: A 266 MET cc_start: 0.5683 (mmt) cc_final: 0.5040 (mmt) REVERT: A 329 MET cc_start: 0.7424 (mmt) cc_final: 0.7099 (mmt) REVERT: A 1054 MET cc_start: 0.8239 (tpp) cc_final: 0.7693 (tpp) REVERT: A 1221 MET cc_start: 0.8275 (tmm) cc_final: 0.7757 (tmm) REVERT: A 1239 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.5625 (t80) REVERT: A 1412 MET cc_start: 0.8724 (ttp) cc_final: 0.8248 (tmm) REVERT: B 550 MET cc_start: 0.7764 (tmm) cc_final: 0.6913 (tmm) REVERT: B 954 MET cc_start: 0.8321 (mtp) cc_final: 0.8074 (ttt) REVERT: C 66 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7751 (t70) REVERT: C 214 ASP cc_start: 0.8044 (m-30) cc_final: 0.7711 (p0) REVERT: D 34 ASN cc_start: 0.2595 (OUTLIER) cc_final: 0.2245 (t0) REVERT: D 67 TYR cc_start: 0.4601 (t80) cc_final: 0.4077 (t80) REVERT: E 48 PRO cc_start: 0.7767 (Cg_endo) cc_final: 0.7564 (Cg_exo) REVERT: G 28 GLN cc_start: 0.8064 (pt0) cc_final: 0.7803 (tm-30) REVERT: G 131 MET cc_start: 0.5778 (mmt) cc_final: 0.3974 (tmm) REVERT: K 34 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8432 (p) REVERT: d 59 MET cc_start: 0.0186 (tpt) cc_final: -0.0380 (ttp) REVERT: f 45 ARG cc_start: -0.1125 (ttt-90) cc_final: -0.2057 (mmt-90) REVERT: h 62 MET cc_start: 0.0848 (OUTLIER) cc_final: 0.0536 (tmm) outliers start: 48 outliers final: 35 residues processed: 209 average time/residue: 0.2514 time to fit residues: 92.0268 Evaluate side-chains 205 residues out of total 4025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1239 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain h residue 42 TYR Chi-restraints excluded: chain h residue 62 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 296 optimal weight: 0.0470 chunk 57 optimal weight: 0.9980 chunk 376 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 21 optimal weight: 0.0000 chunk 366 optimal weight: 10.0000 chunk 357 optimal weight: 30.0000 chunk 269 optimal weight: 1.9990 chunk 462 optimal weight: 20.0000 chunk 317 optimal weight: 8.9990 chunk 387 optimal weight: 20.0000 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** h 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.088708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.064975 restraints weight = 208450.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.064217 restraints weight = 159235.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.064362 restraints weight = 171622.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.064367 restraints weight = 128991.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.064555 restraints weight = 112124.337| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44554 Z= 0.141 Angle : 0.563 14.208 61542 Z= 0.299 Chirality : 0.040 0.174 6924 Planarity : 0.004 0.050 6824 Dihedral : 21.610 161.483 8543 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.15 % Allowed : 12.77 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.13), residues: 4528 helix: 1.78 (0.12), residues: 1870 sheet: -0.28 (0.21), residues: 576 loop : -0.37 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 140 TYR 0.018 0.001 TYR L 41 PHE 0.016 0.001 PHE G 44 TRP 0.022 0.002 TRP C 49 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00318 (44523) covalent geometry : angle 0.55142 (61503) hydrogen bonds : bond 0.03579 ( 2111) hydrogen bonds : angle 4.12966 ( 5705) metal coordination : bond 0.00758 ( 31) metal coordination : angle 4.62091 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7179.53 seconds wall clock time: 124 minutes 53.90 seconds (7493.90 seconds total)