Starting phenix.real_space_refine on Tue Aug 26 17:29:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oeu_16835/08_2025/8oeu_16835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oeu_16835/08_2025/8oeu_16835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oeu_16835/08_2025/8oeu_16835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oeu_16835/08_2025/8oeu_16835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oeu_16835/08_2025/8oeu_16835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oeu_16835/08_2025/8oeu_16835.map" } resolution = 3.04 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= 0.011 sd= 1.105 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 77 5.49 5 Mg 1 5.21 5 S 229 5.16 5 C 24507 2.51 5 N 6872 2.21 5 O 7484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s 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: 39178 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11159 Classifications: {'peptide': 1409} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1340} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9047 Classifications: {'peptide': 1131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 932 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 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: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 549 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 280 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 769 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "S" Number of atoms: 6703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6703 Classifications: {'peptide': 819} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 785} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 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 472 SG CYS A 71 67.017 102.069 89.853 1.00 87.16 S ATOM 494 SG CYS A 74 70.587 100.579 89.146 1.00 88.84 S ATOM 541 SG CYS A 81 68.736 99.658 92.389 1.00 76.23 S ATOM 776 SG CYS A 111 80.130 137.701 117.650 1.00133.12 S ATOM 804 SG CYS A 114 82.853 138.309 115.347 1.00133.39 S ATOM 1117 SG CYS A 154 82.956 139.400 119.066 1.00157.16 S ATOM 1144 SG CYS A 184 81.013 141.413 116.442 1.00156.73 S ATOM 19775 SG CYS B1196 83.723 109.793 92.166 1.00 76.17 S ATOM 19797 SG CYS B1199 81.720 110.665 95.282 1.00 73.22 S ATOM 19912 SG CYS B1214 80.035 110.332 91.944 1.00 82.27 S ATOM 19933 SG CYS B1217 82.347 113.355 92.761 1.00 85.65 S ATOM 20900 SG CYS C 88 58.821 33.946 96.989 1.00 69.48 S ATOM 20913 SG CYS C 90 56.585 36.927 96.096 1.00 74.17 S ATOM 20948 SG CYS C 94 55.272 33.449 96.924 1.00 61.39 S ATOM 20970 SG CYS C 97 56.722 35.773 99.671 1.00 55.31 S ATOM 28739 SG CYS I 86 60.516 86.029 189.860 1.00 89.50 S ATOM 28763 SG CYS I 89 57.393 84.562 191.263 1.00 95.73 S ATOM 28967 SG CYS I 114 57.751 84.468 187.534 1.00 82.11 S ATOM 29002 SG CYS I 119 57.025 87.685 189.481 1.00 99.80 S ATOM 28187 SG CYS I 17 53.142 128.290 176.772 1.00130.77 S ATOM 28211 SG CYS I 20 51.675 128.364 173.250 1.00128.31 S ATOM 28362 SG CYS I 39 55.266 128.923 173.471 1.00138.21 S ATOM 28387 SG CYS I 42 52.890 131.557 174.935 1.00144.02 S ATOM 29112 SG CYS J 7 59.556 41.893 130.205 1.00 27.19 S ATOM 29136 SG CYS J 10 61.116 38.557 129.255 1.00 29.78 S ATOM 29400 SG CYS J 44 62.130 40.465 132.586 1.00 33.85 S ATOM 29406 SG CYS J 45 59.047 38.454 132.086 1.00 33.59 S ATOM 30543 SG CYS L 19 27.145 66.291 113.670 1.00 84.77 S ATOM 30562 SG CYS L 22 24.297 63.888 113.746 1.00 87.92 S ATOM 30673 SG CYS L 36 24.204 66.568 111.252 1.00 93.18 S ATOM 30699 SG CYS L 39 23.685 67.332 115.069 1.00 95.96 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N GLY S1173 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1173 " occ=0.00 residue: pdb=" N GLY S1227 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1227 " occ=0.00 residue: pdb=" N GLY S1235 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1235 " occ=0.00 residue: pdb=" N GLY S1238 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1238 " occ=0.00 residue: pdb=" N GLY S1260 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY S1260 " occ=0.00 Time building chain proxies: 6.86, per 1000 atoms: 0.18 Number of scatterers: 39178 At special positions: 0 Unit cell: (154.35, 163.8, 201.6, 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 229 16.00 P 77 15.00 Mg 1 11.99 O 7484 8.00 N 6872 7.00 C 24507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 184 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1196 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1217 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " 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 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8842 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 51 sheets defined 43.6% alpha, 17.1% beta 24 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.550A pdb=" N VAL A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LYS A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.562A pdb=" N LYS A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 148 removed outlier: 3.686A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.709A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.766A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) 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: 3.523A 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 Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.828A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 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: 3.658A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.555A 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: 3.569A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.273A 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 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.658A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.632A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 3.895A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.832A pdb=" N THR A1184 " --> pdb=" O PRO A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.876A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 removed outlier: 3.652A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.754A pdb=" N LYS A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A1318 " --> pdb=" O ASP A1315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1318' Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 removed outlier: 3.567A pdb=" N VAL A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.894A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1444 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.645A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 3.632A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 98 through 114 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 371 through 385 removed outlier: 3.760A pdb=" N MET B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.576A pdb=" N LYS B 438 " --> pdb=" O CYS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 472 through 502 removed outlier: 3.767A pdb=" N ARG B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 535 through 539 removed outlier: 3.916A pdb=" N ALA B 539 " --> pdb=" O ALA B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.738A pdb=" N ALA B 639 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.500A pdb=" N ILE B 717 " --> pdb=" O LYS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 744 through 748 Processing helix chain 'B' and resid 755 through 760 removed outlier: 4.013A pdb=" N LEU B 759 " --> pdb=" O THR B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 807 through 809 No H-bonds generated for 'chain 'B' and resid 807 through 809' Processing helix chain 'B' and resid 838 through 843 Processing helix chain 'B' and resid 875 through 880 Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.887A pdb=" N LEU B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1154 through 1158 removed outlier: 3.540A pdb=" N ARG B1157 " --> pdb=" O GLY B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1230 through 1241 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.503A pdb=" N CYS C 88 " --> pdb=" O SER C 85 " (cutoff:3.500A) 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 129 through 133 removed outlier: 3.563A pdb=" N ARG C 133 " --> pdb=" O VAL C 130 " (cutoff:3.500A) 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 270 removed outlier: 3.543A pdb=" N ASP C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.617A pdb=" N ALA D 93 " --> pdb=" O GLN D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 118 through 132 Processing helix chain 'D' and resid 135 through 144 removed outlier: 3.990A pdb=" N ALA D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 Processing helix chain 'D' and resid 165 through 180 removed outlier: 3.586A pdb=" N ARG D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.551A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.783A 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 122 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 6.358A pdb=" N THR E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 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 removed outlier: 3.791A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 4.155A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.702A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 107 removed outlier: 4.008A pdb=" N GLU I 105 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.722A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.774A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'S' and resid 285 through 292 Processing helix chain 'S' and resid 295 through 300 removed outlier: 3.591A pdb=" N GLN S 299 " --> pdb=" O PRO S 295 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 324 removed outlier: 3.669A pdb=" N ALA S 317 " --> pdb=" O LEU S 313 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP S 319 " --> pdb=" O GLU S 315 " (cutoff:3.500A) Processing helix chain 'S' and resid 354 through 368 removed outlier: 4.109A pdb=" N LYS S 358 " --> pdb=" O SER S 354 " (cutoff:3.500A) Processing helix chain 'S' and resid 372 through 380 removed outlier: 3.585A pdb=" N TYR S 379 " --> pdb=" O PHE S 375 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 384 Processing helix chain 'S' and resid 389 through 425 removed outlier: 3.593A pdb=" N GLU S 401 " --> pdb=" O TRP S 397 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU S 416 " --> pdb=" O ASN S 412 " (cutoff:3.500A) Processing helix chain 'S' and resid 444 through 453 removed outlier: 3.650A pdb=" N MET S 448 " --> pdb=" O ASP S 444 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU S 451 " --> pdb=" O ASP S 447 " (cutoff:3.500A) Processing helix chain 'S' and resid 456 through 471 WARNING: missing atoms! removed outlier: 3.611A pdb=" N TYR S 470 " --> pdb=" O HIS S 466 " (cutoff:3.500A) Processing helix chain 'S' and resid 475 through 480 removed outlier: 3.959A pdb=" N GLN S 479 " --> pdb=" O ILE S 475 " (cutoff:3.500A) Processing helix chain 'S' and resid 523 through 530 Processing helix chain 'S' and resid 532 through 538 Processing helix chain 'S' and resid 542 through 553 Processing helix chain 'S' and resid 565 through 571 Processing helix chain 'S' and resid 582 through 598 removed outlier: 3.885A pdb=" N MET S 591 " --> pdb=" O GLY S 587 " (cutoff:3.500A) Processing helix chain 'S' and resid 599 through 613 removed outlier: 3.528A pdb=" N VAL S 605 " --> pdb=" O LEU S 601 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU S 612 " --> pdb=" O GLN S 608 " (cutoff:3.500A) Processing helix chain 'S' and resid 623 through 628 removed outlier: 3.551A pdb=" N ASP S 627 " --> pdb=" O LYS S 623 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL S 628 " --> pdb=" O GLY S 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 623 through 628' Processing helix chain 'S' and resid 634 through 638 removed outlier: 3.601A pdb=" N PHE S 637 " --> pdb=" O ALA S 634 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS S 638 " --> pdb=" O TYR S 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 634 through 638' Processing helix chain 'S' and resid 646 through 648 No H-bonds generated for 'chain 'S' and resid 646 through 648' Processing helix chain 'S' and resid 651 through 663 removed outlier: 3.525A pdb=" N LYS S 655 " --> pdb=" O ASP S 651 " (cutoff:3.500A) Processing helix chain 'S' and resid 684 through 690 Processing helix chain 'S' and resid 691 through 694 removed outlier: 3.564A pdb=" N TYR S 694 " --> pdb=" O GLN S 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 691 through 694' Processing helix chain 'S' and resid 699 through 720 removed outlier: 3.779A pdb=" N GLU S 714 " --> pdb=" O THR S 710 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG S 715 " --> pdb=" O MET S 711 " (cutoff:3.500A) Processing helix chain 'S' and resid 720 through 754 removed outlier: 3.849A pdb=" N LEU S 749 " --> pdb=" O CYS S 745 " (cutoff:3.500A) Processing helix chain 'S' and resid 825 through 841 removed outlier: 3.554A pdb=" N ALA S 830 " --> pdb=" O ARG S 826 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN S 831 " --> pdb=" O GLU S 827 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU S 836 " --> pdb=" O ASP S 832 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS S 837 " --> pdb=" O ILE S 833 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS S 838 " --> pdb=" O GLU S 834 " (cutoff:3.500A) Processing helix chain 'S' and resid 856 through 870 removed outlier: 4.479A pdb=" N GLU S 862 " --> pdb=" O GLN S 858 " (cutoff:3.500A) Processing helix chain 'S' and resid 887 through 896 removed outlier: 3.732A pdb=" N LEU S 892 " --> pdb=" O GLU S 888 " (cutoff:3.500A) Processing helix chain 'S' and resid 896 through 903 removed outlier: 3.548A pdb=" N GLU S 900 " --> pdb=" O SER S 896 " (cutoff:3.500A) Processing helix chain 'S' and resid 907 through 920 removed outlier: 3.744A pdb=" N SER S 915 " --> pdb=" O ARG S 911 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU S 916 " --> pdb=" O GLN S 912 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA S 917 " --> pdb=" O ALA S 913 " (cutoff:3.500A) Processing helix chain 'S' and resid 922 through 931 removed outlier: 3.811A pdb=" N GLU S 926 " --> pdb=" O ASP S 922 " (cutoff:3.500A) Processing helix chain 'S' and resid 933 through 939 Processing helix chain 'S' and resid 945 through 949 removed outlier: 3.912A pdb=" N VAL S 949 " --> pdb=" O GLN S 946 " (cutoff:3.500A) Processing helix chain 'S' and resid 950 through 970 removed outlier: 3.925A pdb=" N GLU S 961 " --> pdb=" O ALA S 957 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN S 967 " --> pdb=" O ILE S 963 " (cutoff:3.500A) Processing helix chain 'S' and resid 973 through 979 removed outlier: 3.686A pdb=" N ALA S 978 " --> pdb=" O ASN S 974 " (cutoff:3.500A) Processing helix chain 'S' and resid 980 through 989 removed outlier: 4.692A pdb=" N ALA S 984 " --> pdb=" O TYR S 981 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU S 985 " --> pdb=" O SER S 982 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE S 986 " --> pdb=" O GLN S 983 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN S 987 " --> pdb=" O ALA S 984 " (cutoff:3.500A) Processing helix chain 'S' and resid 995 through 1008 Processing helix chain 'S' and resid 1013 through 1019 removed outlier: 3.908A pdb=" N LEU S1017 " --> pdb=" O SER S1013 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL S1018 " --> pdb=" O ARG S1014 " (cutoff:3.500A) Processing helix chain 'S' and resid 1024 through 1032 removed outlier: 3.674A pdb=" N ASN S1030 " --> pdb=" O LYS S1026 " (cutoff:3.500A) Processing helix chain 'S' and resid 1051 through 1056 Processing helix chain 'S' and resid 1062 through 1072 removed outlier: 3.540A pdb=" N ASP S1072 " --> pdb=" O LYS S1068 " (cutoff:3.500A) Processing helix chain 'S' and resid 1086 through 1089 Processing helix chain 'S' and resid 1090 through 1095 removed outlier: 3.831A pdb=" N ASN S1095 " --> pdb=" O GLU S1091 " (cutoff:3.500A) Processing helix chain 'S' and resid 1103 through 1114 removed outlier: 3.532A pdb=" N GLU S1109 " --> pdb=" O ASP S1105 " (cutoff:3.500A) Processing helix chain 'S' and resid 1119 through 1132 removed outlier: 3.608A pdb=" N TYR S1124 " --> pdb=" O HIS S1120 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER S1131 " --> pdb=" O ARG S1127 " (cutoff:3.500A) Processing helix chain 'S' and resid 1145 through 1155 Processing helix chain 'S' and resid 1241 through 1245 Processing helix chain 'S' and resid 1282 through 1286 removed outlier: 3.556A pdb=" N LEU S1286 " --> pdb=" O THR S1283 " (cutoff:3.500A) 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 47 through 48 removed outlier: 3.989A pdb=" N ARG A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.282A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.180A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.235A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.733A pdb=" N LEU B1161 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1137 through 1139 removed outlier: 7.746A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.852A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.161A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.649A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.804A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=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: 4.157A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1243 through 1248 removed outlier: 4.432A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.393A 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 1408 through 1409 removed outlier: 8.387A pdb=" N GLY A1409 " --> pdb=" O GLN E 174 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC1, first strand: chain 'B' and resid 142 through 145 removed outlier: 5.457A pdb=" N TYR B 161 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 210 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU B 163 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR B 208 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE B 165 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B 206 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 167 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ALA B 199 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS B 228 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 201 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 205 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN B 222 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LYS B 207 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLN B 220 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL B 209 " --> pdb=" O GLN B 218 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN B 218 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LYS B 211 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN B 216 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AC3, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AC4, first strand: chain 'B' and resid 468 through 471 Processing sheet with id=AC5, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.573A pdb=" N TYR B 294 " --> pdb=" O MET B 316 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AC7, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AC8, first strand: chain 'B' and resid 628 through 629 removed outlier: 5.394A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.659A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.659A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL B 984 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AD3, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.451A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 905 through 906 Processing sheet with id=AD5, first strand: chain 'B' and resid 942 through 944 Processing sheet with id=AD6, first strand: chain 'B' and resid 1190 through 1196 Processing sheet with id=AD7, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AD8, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.289A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.844A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.438A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.184A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'G' and resid 2 through 13 removed outlier: 6.915A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.610A pdb=" N VAL G 58 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 83 through 86 removed outlier: 5.223A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.506A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 25 through 29 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 Processing sheet with id=AF2, first strand: chain 'S' and resid 640 through 644 removed outlier: 5.443A pdb=" N LYS S 641 " --> pdb=" O ILE S 618 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE S 618 " --> pdb=" O LYS S 641 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS S 643 " --> pdb=" O LEU S 616 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 805 through 811 removed outlier: 4.139A pdb=" N ASP S 807 " --> pdb=" O LEU S 798 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL S 794 " --> pdb=" O LEU S 811 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA S 797 " --> pdb=" O GLY S 783 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL S 781 " --> pdb=" O VAL S 799 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 971 through 972 removed outlier: 5.868A pdb=" N VAL S 971 " --> pdb=" O LYS S1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'S' and resid 1166 through 1167 Processing sheet with id=AF6, first strand: chain 'S' and resid 1170 through 1171 removed outlier: 3.697A pdb=" N VAL S1228 " --> pdb=" O ILE S1240 " (cutoff:3.500A) 1684 hydrogen bonds defined for protein. 4677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 10.70 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9742 1.33 - 1.45: 8138 1.45 - 1.58: 21675 1.58 - 1.70: 151 1.70 - 1.82: 361 Bond restraints: 40067 Sorted by residual: bond pdb=" C LEU S 860 " pdb=" O LEU S 860 " ideal model delta sigma weight residual 1.236 1.316 -0.080 1.29e-02 6.01e+03 3.85e+01 bond pdb=" C ASP S 863 " pdb=" O ASP S 863 " ideal model delta sigma weight residual 1.236 1.277 -0.041 1.15e-02 7.56e+03 1.25e+01 bond pdb=" N GLU B 904 " pdb=" CA GLU B 904 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.25e-02 6.40e+03 9.29e+00 bond pdb=" N VAL S 864 " pdb=" CA VAL S 864 " ideal model delta sigma weight residual 1.459 1.497 -0.037 1.33e-02 5.65e+03 7.92e+00 bond pdb=" C ILE S 861 " pdb=" O ILE S 861 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.13e-02 7.83e+03 7.38e+00 ... (remaining 40062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 53748 3.22 - 6.44: 592 6.44 - 9.66: 78 9.66 - 12.88: 5 12.88 - 16.09: 2 Bond angle restraints: 54425 Sorted by residual: angle pdb=" N ILE S 867 " pdb=" CA ILE S 867 " pdb=" C ILE S 867 " ideal model delta sigma weight residual 110.62 103.06 7.56 1.02e+00 9.61e-01 5.49e+01 angle pdb=" CG ARG A 483 " pdb=" CD ARG A 483 " pdb=" NE ARG A 483 " ideal model delta sigma weight residual 112.00 128.09 -16.09 2.20e+00 2.07e-01 5.35e+01 angle pdb=" C ASP S 863 " pdb=" N VAL S 864 " pdb=" CA VAL S 864 " ideal model delta sigma weight residual 120.64 110.01 10.63 1.64e+00 3.72e-01 4.20e+01 angle pdb=" N HIS S 869 " pdb=" CA HIS S 869 " pdb=" C HIS S 869 " ideal model delta sigma weight residual 111.75 103.52 8.23 1.28e+00 6.10e-01 4.14e+01 angle pdb=" N LEU S 860 " pdb=" CA LEU S 860 " pdb=" C LEU S 860 " ideal model delta sigma weight residual 112.54 105.12 7.42 1.22e+00 6.72e-01 3.70e+01 ... (remaining 54420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 23590 32.78 - 65.57: 708 65.57 - 98.35: 71 98.35 - 131.14: 0 131.14 - 163.92: 1 Dihedral angle restraints: 24370 sinusoidal: 10720 harmonic: 13650 Sorted by residual: dihedral pdb=" CA GLU S1156 " pdb=" C GLU S1156 " pdb=" N THR S1157 " pdb=" CA THR S1157 " ideal model delta harmonic sigma weight residual -180.00 -141.07 -38.93 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA GLN A 539 " pdb=" C GLN A 539 " pdb=" N ASP A 540 " pdb=" CA ASP A 540 " ideal model delta harmonic sigma weight residual 180.00 142.20 37.80 0 5.00e+00 4.00e-02 5.72e+01 dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual 180.00 144.91 35.09 0 5.00e+00 4.00e-02 4.93e+01 ... (remaining 24367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5687 0.104 - 0.208: 357 0.208 - 0.312: 21 0.312 - 0.416: 4 0.416 - 0.520: 2 Chirality restraints: 6071 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" CA ASN G 124 " pdb=" N ASN G 124 " pdb=" C ASN G 124 " pdb=" CB ASN G 124 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA LYS B 897 " pdb=" N LYS B 897 " pdb=" C LYS B 897 " pdb=" CB LYS B 897 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 6068 not shown) Planarity restraints: 6777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 167 " -0.038 2.00e-02 2.50e+03 3.92e-02 3.08e+01 pdb=" CG TYR G 167 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 TYR G 167 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR G 167 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR G 167 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR G 167 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR G 167 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 167 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 140 " 0.075 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO B 141 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS S 844 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO S 845 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO S 845 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO S 845 " 0.058 5.00e-02 4.00e+02 ... (remaining 6774 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 517 2.64 - 3.20: 33857 3.20 - 3.77: 63934 3.77 - 4.33: 91117 4.33 - 4.90: 146056 Nonbonded interactions: 335481 Sorted by model distance: nonbonded pdb=" NZ LYS E 115 " pdb=" OE1 GLN E 129 " model vdw 2.072 3.120 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.091 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.106 2.170 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2001 " model vdw 2.140 2.170 nonbonded pdb=" OE1 GLU S1156 " pdb=" OG1 THR S1160 " model vdw 2.193 3.040 ... (remaining 335476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 40.430 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 0.101 40099 Z= 0.279 Angle : 0.912 16.095 54470 Z= 0.511 Chirality : 0.055 0.520 6071 Planarity : 0.006 0.109 6777 Dihedral : 15.252 163.920 15528 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.10 % Allowed : 0.65 % Favored : 99.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.07 % 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: -1.32 (0.12), residues: 4612 helix: -0.99 (0.11), residues: 1786 sheet: -0.54 (0.19), residues: 659 loop : -0.71 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 875 TYR 0.093 0.003 TYR G 167 PHE 0.044 0.003 PHE A 431 TRP 0.028 0.003 TRP A 479 HIS 0.013 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00635 (40067) covalent geometry : angle 0.90278 (54425) hydrogen bonds : bond 0.18020 ( 1714) hydrogen bonds : angle 7.43748 ( 4795) metal coordination : bond 0.00879 ( 32) metal coordination : angle 4.53535 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 647 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7626 (mtm180) cc_final: 0.7406 (mtm180) REVERT: A 266 MET cc_start: 0.4254 (mmp) cc_final: 0.3981 (mmp) REVERT: A 330 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7318 (tp40) REVERT: A 1284 PHE cc_start: 0.7938 (t80) cc_final: 0.7576 (t80) REVERT: A 1288 ILE cc_start: 0.8818 (pt) cc_final: 0.8554 (mm) REVERT: A 1437 ASP cc_start: 0.7736 (m-30) cc_final: 0.7507 (m-30) REVERT: B 417 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7518 (mtmt) REVERT: B 418 GLU cc_start: 0.6943 (tp30) cc_final: 0.6552 (tm-30) REVERT: B 495 TYR cc_start: 0.7076 (t80) cc_final: 0.6792 (t80) REVERT: B 574 LYS cc_start: 0.8096 (mmmm) cc_final: 0.7462 (ptmm) REVERT: B 762 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7406 (ttmt) REVERT: E 9 ARG cc_start: 0.7582 (mtt-85) cc_final: 0.7284 (mtt-85) REVERT: E 90 TYR cc_start: 0.8114 (m-80) cc_final: 0.7732 (m-80) REVERT: G 117 MET cc_start: 0.7827 (mmt) cc_final: 0.7331 (mmt) REVERT: G 165 ASP cc_start: 0.7217 (m-30) cc_final: 0.6805 (m-30) REVERT: H 4 ILE cc_start: 0.9145 (mm) cc_final: 0.8936 (mm) REVERT: H 65 TYR cc_start: 0.8112 (m-10) cc_final: 0.7880 (m-10) REVERT: I 22 ASN cc_start: 0.7983 (m-40) cc_final: 0.7549 (m110) REVERT: K 93 ASP cc_start: 0.7882 (m-30) cc_final: 0.7517 (m-30) REVERT: L 46 LYS cc_start: 0.9091 (mtpp) cc_final: 0.8812 (mtpt) REVERT: S 924 LEU cc_start: 0.8593 (tp) cc_final: 0.8389 (tp) REVERT: S 1069 MET cc_start: 0.6926 (mmp) cc_final: 0.6697 (mmm) outliers start: 4 outliers final: 0 residues processed: 651 average time/residue: 0.2405 time to fit residues: 244.2618 Evaluate side-chains 487 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 486 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 762 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 GLN A1194 ASN B 538 GLN B 726 ASN B 902 GLN C 157 GLN D 118 ASN H 131 ASN I 74 GLN J 61 ASN K 89 ASN L 26 ASN S 608 GLN S 842 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.163548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130916 restraints weight = 68936.047| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.29 r_work: 0.3370 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40099 Z= 0.168 Angle : 0.611 11.210 54470 Z= 0.320 Chirality : 0.044 0.207 6071 Planarity : 0.005 0.076 6777 Dihedral : 12.218 169.678 5988 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.82 % Allowed : 6.69 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.12), residues: 4612 helix: -0.02 (0.12), residues: 1817 sheet: -0.48 (0.19), residues: 662 loop : -0.46 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 483 TYR 0.029 0.002 TYR G 167 PHE 0.026 0.002 PHE A 112 TRP 0.015 0.002 TRP A 479 HIS 0.007 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00377 (40067) covalent geometry : angle 0.60079 (54425) hydrogen bonds : bond 0.04643 ( 1714) hydrogen bonds : angle 5.34190 ( 4795) metal coordination : bond 0.00614 ( 32) metal coordination : angle 3.88849 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 524 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TRP cc_start: 0.6668 (m-90) cc_final: 0.6414 (m-90) REVERT: A 917 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8320 (mm-30) REVERT: A 1153 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7675 (mtp180) REVERT: A 1284 PHE cc_start: 0.7908 (t80) cc_final: 0.7606 (t80) REVERT: A 1303 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7253 (mp10) REVERT: A 1437 ASP cc_start: 0.8376 (m-30) cc_final: 0.8169 (m-30) REVERT: B 418 GLU cc_start: 0.7377 (tp30) cc_final: 0.6699 (tm-30) REVERT: B 495 TYR cc_start: 0.7329 (t80) cc_final: 0.6992 (t80) REVERT: B 515 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7653 (mtm110) REVERT: B 574 LYS cc_start: 0.8288 (mmmm) cc_final: 0.7504 (ttpt) REVERT: B 762 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7559 (ttmt) REVERT: C 164 TYR cc_start: 0.9166 (m-80) cc_final: 0.8944 (m-80) REVERT: E 90 TYR cc_start: 0.8207 (m-80) cc_final: 0.7847 (m-80) REVERT: G 21 ASN cc_start: 0.8437 (p0) cc_final: 0.8083 (p0) REVERT: G 117 MET cc_start: 0.8127 (mmt) cc_final: 0.7869 (mmt) REVERT: H 4 ILE cc_start: 0.9137 (mm) cc_final: 0.8927 (mm) REVERT: H 81 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7341 (ttp-110) REVERT: I 25 TYR cc_start: 0.7618 (m-80) cc_final: 0.6867 (m-80) REVERT: I 40 ARG cc_start: 0.7975 (ptp-170) cc_final: 0.7579 (ptt180) REVERT: J 28 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8311 (mm-30) REVERT: J 55 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8868 (tt) REVERT: K 93 ASP cc_start: 0.8483 (m-30) cc_final: 0.8156 (m-30) REVERT: L 52 LEU cc_start: 0.8668 (mt) cc_final: 0.8428 (mp) outliers start: 34 outliers final: 20 residues processed: 542 average time/residue: 0.2431 time to fit residues: 208.0359 Evaluate side-chains 498 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 476 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain S residue 389 HIS Chi-restraints excluded: chain S residue 868 VAL Chi-restraints excluded: chain S residue 906 TYR Chi-restraints excluded: chain S residue 934 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 65 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 363 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 460 optimal weight: 3.9990 chunk 304 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 414 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1042 ASN B1178 GLN C 157 GLN E 30 GLN H 29 HIS I 74 GLN I 84 HIS ** S 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.163886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132129 restraints weight = 68446.512| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.09 r_work: 0.3390 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40099 Z= 0.149 Angle : 0.562 10.472 54470 Z= 0.293 Chirality : 0.043 0.191 6071 Planarity : 0.004 0.059 6777 Dihedral : 12.041 168.345 5988 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.11 % Allowed : 9.18 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.12), residues: 4612 helix: 0.39 (0.12), residues: 1830 sheet: -0.43 (0.19), residues: 656 loop : -0.37 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 334 TYR 0.017 0.001 TYR G 167 PHE 0.029 0.002 PHE A 112 TRP 0.015 0.001 TRP B 104 HIS 0.007 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00339 (40067) covalent geometry : angle 0.55340 (54425) hydrogen bonds : bond 0.04080 ( 1714) hydrogen bonds : angle 5.03621 ( 4795) metal coordination : bond 0.00512 ( 32) metal coordination : angle 3.46477 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 526 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 202 TRP cc_start: 0.6549 (m-90) cc_final: 0.6289 (m-90) REVERT: A 712 ASP cc_start: 0.7960 (m-30) cc_final: 0.7740 (m-30) REVERT: A 917 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8194 (mm-30) REVERT: A 1042 ASN cc_start: 0.9258 (m-40) cc_final: 0.9037 (m-40) REVERT: A 1153 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7635 (mtm180) REVERT: A 1157 ILE cc_start: 0.8677 (mm) cc_final: 0.8401 (mm) REVERT: A 1262 MET cc_start: 0.4842 (mmm) cc_final: 0.4540 (mmm) REVERT: A 1284 PHE cc_start: 0.7920 (t80) cc_final: 0.7429 (t80) REVERT: A 1285 LEU cc_start: 0.8394 (tp) cc_final: 0.8167 (mp) REVERT: A 1288 ILE cc_start: 0.8451 (mm) cc_final: 0.8248 (mm) REVERT: A 1303 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7430 (mp10) REVERT: A 1421 ARG cc_start: 0.8279 (mmt90) cc_final: 0.7727 (mmp-170) REVERT: A 1440 MET cc_start: 0.9117 (mmt) cc_final: 0.8856 (mmt) REVERT: B 418 GLU cc_start: 0.7542 (tp30) cc_final: 0.6696 (tm-30) REVERT: B 495 TYR cc_start: 0.7237 (t80) cc_final: 0.6905 (t80) REVERT: B 515 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7673 (mtm110) REVERT: B 574 LYS cc_start: 0.8270 (mmmm) cc_final: 0.7461 (ttpt) REVERT: B 974 ARG cc_start: 0.7170 (mtp85) cc_final: 0.6964 (mtt180) REVERT: E 9 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7328 (mtt-85) REVERT: E 90 TYR cc_start: 0.8263 (m-80) cc_final: 0.7915 (m-80) REVERT: G 21 ASN cc_start: 0.8392 (p0) cc_final: 0.8120 (p0) REVERT: G 117 MET cc_start: 0.8206 (mmt) cc_final: 0.7928 (mmt) REVERT: H 4 ILE cc_start: 0.9109 (mm) cc_final: 0.8900 (mm) REVERT: H 66 GLU cc_start: 0.7710 (mp0) cc_final: 0.7300 (mp0) REVERT: I 22 ASN cc_start: 0.7985 (m110) cc_final: 0.7656 (m-40) REVERT: I 25 TYR cc_start: 0.7610 (m-80) cc_final: 0.6799 (m-80) REVERT: I 40 ARG cc_start: 0.7933 (ptp-170) cc_final: 0.7478 (ptt180) REVERT: I 125 GLU cc_start: 0.6968 (mp0) cc_final: 0.6718 (mp0) REVERT: K 93 ASP cc_start: 0.8444 (m-30) cc_final: 0.8119 (m-30) REVERT: L 29 LYS cc_start: 0.6753 (mmpt) cc_final: 0.6429 (mmpt) REVERT: L 50 LYS cc_start: 0.8749 (mmtm) cc_final: 0.8453 (mmtm) REVERT: L 52 LEU cc_start: 0.8654 (mt) cc_final: 0.8404 (mp) REVERT: S 591 MET cc_start: 0.8388 (mtt) cc_final: 0.8042 (mtt) outliers start: 46 outliers final: 28 residues processed: 551 average time/residue: 0.2293 time to fit residues: 200.1694 Evaluate side-chains 504 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 476 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain S residue 389 HIS Chi-restraints excluded: chain S residue 782 LEU Chi-restraints excluded: chain S residue 792 HIS Chi-restraints excluded: chain S residue 934 ASP Chi-restraints excluded: chain S residue 973 VAL Chi-restraints excluded: chain S residue 1130 LEU Chi-restraints excluded: chain S residue 1236 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 349 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 419 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 391 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1299 GLN B 194 ASN C 157 GLN L 23 HIS ** S 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.162998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131019 restraints weight = 68336.473| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.18 r_work: 0.3351 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40099 Z= 0.186 Angle : 0.575 11.411 54470 Z= 0.298 Chirality : 0.044 0.199 6071 Planarity : 0.004 0.058 6777 Dihedral : 12.002 168.466 5988 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.79 % Allowed : 10.43 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.12), residues: 4612 helix: 0.54 (0.12), residues: 1837 sheet: -0.45 (0.19), residues: 654 loop : -0.39 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 734 TYR 0.019 0.002 TYR I 54 PHE 0.030 0.002 PHE A 112 TRP 0.016 0.002 TRP B 104 HIS 0.006 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00430 (40067) covalent geometry : angle 0.56626 (54425) hydrogen bonds : bond 0.04041 ( 1714) hydrogen bonds : angle 4.94173 ( 4795) metal coordination : bond 0.00606 ( 32) metal coordination : angle 3.51713 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 501 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: A 202 TRP cc_start: 0.6483 (m-90) cc_final: 0.6220 (m-90) REVERT: A 637 MET cc_start: 0.9278 (ptp) cc_final: 0.9028 (ptp) REVERT: A 712 ASP cc_start: 0.7941 (m-30) cc_final: 0.7725 (m-30) REVERT: A 1153 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7657 (mtm180) REVERT: A 1157 ILE cc_start: 0.8710 (mm) cc_final: 0.8473 (mm) REVERT: A 1236 ASN cc_start: 0.8380 (m-40) cc_final: 0.7905 (t0) REVERT: A 1262 MET cc_start: 0.5117 (mmm) cc_final: 0.4866 (mmm) REVERT: A 1284 PHE cc_start: 0.7920 (t80) cc_final: 0.7402 (t80) REVERT: A 1285 LEU cc_start: 0.8423 (tp) cc_final: 0.8173 (mp) REVERT: A 1421 ARG cc_start: 0.8355 (mmt90) cc_final: 0.7756 (mmp-170) REVERT: B 495 TYR cc_start: 0.7234 (t80) cc_final: 0.6910 (t80) REVERT: B 515 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7618 (mtm110) REVERT: B 574 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7504 (ttpt) REVERT: C 164 TYR cc_start: 0.9227 (m-80) cc_final: 0.8991 (m-80) REVERT: G 117 MET cc_start: 0.8297 (mmt) cc_final: 0.7998 (mmt) REVERT: H 4 ILE cc_start: 0.9138 (mm) cc_final: 0.8914 (mm) REVERT: H 66 GLU cc_start: 0.7668 (mp0) cc_final: 0.7285 (mp0) REVERT: I 22 ASN cc_start: 0.7949 (m110) cc_final: 0.7639 (m-40) REVERT: K 93 ASP cc_start: 0.8497 (m-30) cc_final: 0.8169 (m-30) REVERT: L 29 LYS cc_start: 0.6809 (mmpt) cc_final: 0.6476 (mmpt) REVERT: L 50 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8503 (mmtm) REVERT: L 52 LEU cc_start: 0.8650 (mt) cc_final: 0.8429 (mp) outliers start: 74 outliers final: 48 residues processed: 543 average time/residue: 0.2376 time to fit residues: 206.4647 Evaluate side-chains 529 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 481 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 969 CYS Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain S residue 389 HIS Chi-restraints excluded: chain S residue 721 LEU Chi-restraints excluded: chain S residue 792 HIS Chi-restraints excluded: chain S residue 868 VAL Chi-restraints excluded: chain S residue 934 ASP Chi-restraints excluded: chain S residue 973 VAL Chi-restraints excluded: chain S residue 1120 HIS Chi-restraints excluded: chain S residue 1130 LEU Chi-restraints excluded: chain S residue 1156 GLU Chi-restraints excluded: chain S residue 1236 VAL Chi-restraints excluded: chain S residue 1257 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 340 optimal weight: 3.9990 chunk 439 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 436 optimal weight: 2.9990 chunk 428 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN B 760 GLN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 724 GLN S 731 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.161256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129222 restraints weight = 68498.415| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.39 r_work: 0.3315 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 40099 Z= 0.273 Angle : 0.636 12.476 54470 Z= 0.328 Chirality : 0.046 0.225 6071 Planarity : 0.005 0.063 6777 Dihedral : 12.084 167.829 5988 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.08 % Allowed : 11.62 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.12), residues: 4612 helix: 0.48 (0.12), residues: 1834 sheet: -0.57 (0.19), residues: 649 loop : -0.45 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 24 TYR 0.024 0.002 TYR D 109 PHE 0.029 0.002 PHE A 112 TRP 0.016 0.002 TRP B 104 HIS 0.007 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00637 (40067) covalent geometry : angle 0.62726 (54425) hydrogen bonds : bond 0.04412 ( 1714) hydrogen bonds : angle 5.04437 ( 4795) metal coordination : bond 0.00827 ( 32) metal coordination : angle 3.76285 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 505 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 TRP cc_start: 0.6599 (m-90) cc_final: 0.6303 (m-90) REVERT: A 306 ASP cc_start: 0.8055 (t0) cc_final: 0.7812 (t0) REVERT: A 637 MET cc_start: 0.9290 (ptp) cc_final: 0.9013 (ptp) REVERT: A 1034 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.6874 (tp40) REVERT: A 1153 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7674 (mtm180) REVERT: A 1157 ILE cc_start: 0.8713 (mm) cc_final: 0.8474 (mm) REVERT: A 1236 ASN cc_start: 0.8393 (m-40) cc_final: 0.7907 (t0) REVERT: A 1255 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.5067 (mt) REVERT: A 1262 MET cc_start: 0.5194 (mmm) cc_final: 0.4952 (mmm) REVERT: A 1284 PHE cc_start: 0.7890 (t80) cc_final: 0.7393 (t80) REVERT: A 1285 LEU cc_start: 0.8457 (tp) cc_final: 0.8171 (mp) REVERT: A 1303 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7333 (mp10) REVERT: A 1421 ARG cc_start: 0.8424 (mmt90) cc_final: 0.7800 (mmp-170) REVERT: B 495 TYR cc_start: 0.7250 (t80) cc_final: 0.6905 (t80) REVERT: B 515 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7619 (mtm110) REVERT: B 762 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7533 (ttmt) REVERT: B 1153 GLU cc_start: 0.8153 (tt0) cc_final: 0.7946 (tt0) REVERT: G 117 MET cc_start: 0.8252 (mmt) cc_final: 0.7742 (mmt) REVERT: H 4 ILE cc_start: 0.9202 (mm) cc_final: 0.8979 (mm) REVERT: H 66 GLU cc_start: 0.7758 (mp0) cc_final: 0.7302 (mp0) REVERT: I 22 ASN cc_start: 0.7917 (m110) cc_final: 0.7691 (m-40) REVERT: I 23 MET cc_start: 0.7472 (ttp) cc_final: 0.6550 (tpt) REVERT: K 93 ASP cc_start: 0.8493 (m-30) cc_final: 0.8152 (m-30) REVERT: L 29 LYS cc_start: 0.6849 (mmpt) cc_final: 0.6411 (mmpt) REVERT: L 50 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8589 (mmtm) outliers start: 86 outliers final: 63 residues processed: 558 average time/residue: 0.2576 time to fit residues: 228.1906 Evaluate side-chains 541 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 475 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 969 CYS Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain S residue 300 LEU Chi-restraints excluded: chain S residue 389 HIS Chi-restraints excluded: chain S residue 592 VAL Chi-restraints excluded: chain S residue 747 ARG Chi-restraints excluded: chain S residue 782 LEU Chi-restraints excluded: chain S residue 792 HIS Chi-restraints excluded: chain S residue 868 VAL Chi-restraints excluded: chain S residue 899 SER Chi-restraints excluded: chain S residue 934 ASP Chi-restraints excluded: chain S residue 973 VAL Chi-restraints excluded: chain S residue 1120 HIS Chi-restraints excluded: chain S residue 1130 LEU Chi-restraints excluded: chain S residue 1156 GLU Chi-restraints excluded: chain S residue 1236 VAL Chi-restraints excluded: chain S residue 1257 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 96 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 293 optimal weight: 0.1980 chunk 245 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN J 61 ASN L 23 HIS ** S 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 731 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.163259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131847 restraints weight = 68350.064| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.07 r_work: 0.3362 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40099 Z= 0.149 Angle : 0.555 13.972 54470 Z= 0.286 Chirality : 0.043 0.181 6071 Planarity : 0.004 0.060 6777 Dihedral : 11.982 169.803 5988 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.76 % Allowed : 12.49 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.12), residues: 4612 helix: 0.73 (0.12), residues: 1835 sheet: -0.48 (0.19), residues: 645 loop : -0.34 (0.14), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 734 TYR 0.017 0.001 TYR I 37 PHE 0.029 0.001 PHE A 112 TRP 0.016 0.001 TRP B 104 HIS 0.007 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00342 (40067) covalent geometry : angle 0.54691 (54425) hydrogen bonds : bond 0.03766 ( 1714) hydrogen bonds : angle 4.83515 ( 4795) metal coordination : bond 0.00498 ( 32) metal coordination : angle 3.25686 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 506 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 202 TRP cc_start: 0.6411 (m-90) cc_final: 0.6158 (m-90) REVERT: A 637 MET cc_start: 0.9268 (ptp) cc_final: 0.8960 (ptp) REVERT: A 734 ARG cc_start: 0.7705 (mmt-90) cc_final: 0.7266 (mmt-90) REVERT: A 1034 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.6750 (tp40) REVERT: A 1153 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7701 (mtm180) REVERT: A 1157 ILE cc_start: 0.8669 (mm) cc_final: 0.8431 (mm) REVERT: A 1227 THR cc_start: 0.8773 (t) cc_final: 0.8415 (p) REVERT: A 1236 ASN cc_start: 0.8391 (m-40) cc_final: 0.7859 (t0) REVERT: A 1255 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.5134 (mt) REVERT: A 1262 MET cc_start: 0.5584 (mmm) cc_final: 0.5362 (mmm) REVERT: A 1284 PHE cc_start: 0.7895 (t80) cc_final: 0.7445 (t80) REVERT: A 1285 LEU cc_start: 0.8489 (tp) cc_final: 0.8274 (mp) REVERT: A 1303 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7265 (mp10) REVERT: A 1421 ARG cc_start: 0.8413 (mmt90) cc_final: 0.7927 (mmp-170) REVERT: A 1441 GLU cc_start: 0.8222 (tp30) cc_final: 0.7931 (tp30) REVERT: B 495 TYR cc_start: 0.7267 (t80) cc_final: 0.6968 (t80) REVERT: B 515 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7690 (mtm110) REVERT: B 762 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7655 (ttmt) REVERT: B 972 PHE cc_start: 0.8760 (m-80) cc_final: 0.8560 (m-80) REVERT: B 1235 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8660 (tp) REVERT: C 164 TYR cc_start: 0.9204 (m-80) cc_final: 0.9003 (m-80) REVERT: E 70 ASP cc_start: 0.7698 (t0) cc_final: 0.7335 (t70) REVERT: E 193 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8774 (mp) REVERT: F 98 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8471 (ttpt) REVERT: G 117 MET cc_start: 0.8132 (mmt) cc_final: 0.7691 (mmt) REVERT: H 4 ILE cc_start: 0.9147 (mm) cc_final: 0.8907 (mm) REVERT: H 66 GLU cc_start: 0.7735 (mp0) cc_final: 0.7292 (mp0) REVERT: H 133 HIS cc_start: 0.8162 (m-70) cc_final: 0.7922 (m-70) REVERT: I 47 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7908 (mm-30) REVERT: I 93 GLU cc_start: 0.8467 (tt0) cc_final: 0.8167 (tt0) REVERT: K 93 ASP cc_start: 0.8475 (m-30) cc_final: 0.8153 (m-30) REVERT: L 29 LYS cc_start: 0.6583 (mmpt) cc_final: 0.6342 (mmpt) REVERT: L 50 LYS cc_start: 0.8793 (mmtm) cc_final: 0.8489 (mmtm) REVERT: L 52 LEU cc_start: 0.8634 (mt) cc_final: 0.8394 (mp) outliers start: 73 outliers final: 53 residues processed: 556 average time/residue: 0.2530 time to fit residues: 226.9705 Evaluate side-chains 531 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 472 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 389 HIS Chi-restraints excluded: chain S residue 396 VAL Chi-restraints excluded: chain S residue 454 VAL Chi-restraints excluded: chain S residue 591 MET Chi-restraints excluded: chain S residue 747 ARG Chi-restraints excluded: chain S residue 782 LEU Chi-restraints excluded: chain S residue 792 HIS Chi-restraints excluded: chain S residue 899 SER Chi-restraints excluded: chain S residue 934 ASP Chi-restraints excluded: chain S residue 973 VAL Chi-restraints excluded: chain S residue 1120 HIS Chi-restraints excluded: chain S residue 1130 LEU Chi-restraints excluded: chain S residue 1156 GLU Chi-restraints excluded: chain S residue 1236 VAL Chi-restraints excluded: chain S residue 1257 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 390 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 355 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 385 optimal weight: 5.9990 chunk 305 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN J 61 ASN ** S 561 GLN ** 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 = 0.4005 r_free = 0.4005 target = 0.163424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131749 restraints weight = 68244.511| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.39 r_work: 0.3359 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40099 Z= 0.171 Angle : 0.568 13.308 54470 Z= 0.292 Chirality : 0.043 0.188 6071 Planarity : 0.004 0.060 6777 Dihedral : 11.946 169.357 5988 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.20 % Allowed : 12.75 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.12), residues: 4612 helix: 0.78 (0.12), residues: 1844 sheet: -0.50 (0.19), residues: 651 loop : -0.33 (0.14), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 904 TYR 0.017 0.002 TYR B 292 PHE 0.035 0.002 PHE A 112 TRP 0.016 0.001 TRP B 104 HIS 0.006 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00397 (40067) covalent geometry : angle 0.55977 (54425) hydrogen bonds : bond 0.03823 ( 1714) hydrogen bonds : angle 4.81001 ( 4795) metal coordination : bond 0.00554 ( 32) metal coordination : angle 3.30121 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 492 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 202 TRP cc_start: 0.6390 (m-90) cc_final: 0.6143 (m-90) REVERT: A 248 MET cc_start: 0.8779 (mtt) cc_final: 0.8459 (mtm) REVERT: A 637 MET cc_start: 0.9271 (ptp) cc_final: 0.8948 (ptp) REVERT: A 1034 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.6765 (tp40) REVERT: A 1153 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7729 (mtm180) REVERT: A 1157 ILE cc_start: 0.8675 (mm) cc_final: 0.8434 (mm) REVERT: A 1227 THR cc_start: 0.8788 (t) cc_final: 0.8446 (p) REVERT: A 1234 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8205 (mttm) REVERT: A 1236 ASN cc_start: 0.8410 (m-40) cc_final: 0.7900 (t0) REVERT: A 1284 PHE cc_start: 0.7882 (t80) cc_final: 0.7402 (t80) REVERT: A 1285 LEU cc_start: 0.8390 (tp) cc_final: 0.8176 (mp) REVERT: A 1303 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7307 (mp10) REVERT: A 1325 ASP cc_start: 0.8430 (m-30) cc_final: 0.8106 (t0) REVERT: A 1421 ARG cc_start: 0.8412 (mmt90) cc_final: 0.7996 (mmp-170) REVERT: A 1441 GLU cc_start: 0.8186 (tp30) cc_final: 0.7894 (tp30) REVERT: B 343 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: B 495 TYR cc_start: 0.7305 (t80) cc_final: 0.6965 (t80) REVERT: B 515 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7687 (mtm110) REVERT: B 762 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7610 (ttmt) REVERT: B 972 PHE cc_start: 0.8739 (m-80) cc_final: 0.8515 (m-80) REVERT: B 1235 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8840 (tp) REVERT: E 70 ASP cc_start: 0.7706 (t0) cc_final: 0.7221 (t70) REVERT: E 193 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8777 (mp) REVERT: G 117 MET cc_start: 0.8119 (mmt) cc_final: 0.7667 (mmt) REVERT: H 4 ILE cc_start: 0.9139 (mm) cc_final: 0.8902 (mm) REVERT: H 66 GLU cc_start: 0.7699 (mp0) cc_final: 0.7292 (mp0) REVERT: H 133 HIS cc_start: 0.8135 (m-70) cc_final: 0.7886 (m-70) REVERT: I 23 MET cc_start: 0.7521 (ttp) cc_final: 0.6566 (tpt) REVERT: I 47 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7910 (mm-30) REVERT: K 93 ASP cc_start: 0.8469 (m-30) cc_final: 0.8150 (m-30) REVERT: L 50 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8506 (mmtm) REVERT: L 52 LEU cc_start: 0.8639 (mt) cc_final: 0.8388 (mp) outliers start: 91 outliers final: 65 residues processed: 548 average time/residue: 0.2448 time to fit residues: 216.2155 Evaluate side-chains 545 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 475 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain S residue 300 LEU Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 389 HIS Chi-restraints excluded: chain S residue 396 VAL Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain S residue 454 VAL Chi-restraints excluded: chain S residue 591 MET Chi-restraints excluded: chain S residue 721 LEU Chi-restraints excluded: chain S residue 747 ARG Chi-restraints excluded: chain S residue 782 LEU Chi-restraints excluded: chain S residue 792 HIS Chi-restraints excluded: chain S residue 899 SER Chi-restraints excluded: chain S residue 934 ASP Chi-restraints excluded: chain S residue 1120 HIS Chi-restraints excluded: chain S residue 1130 LEU Chi-restraints excluded: chain S residue 1156 GLU Chi-restraints excluded: chain S residue 1236 VAL Chi-restraints excluded: chain S residue 1257 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 210 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 380 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 333 optimal weight: 0.9990 chunk 314 optimal weight: 0.9990 chunk 348 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN J 61 ASN S 731 ASN S 813 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.162406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131074 restraints weight = 68243.462| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.24 r_work: 0.3346 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 40099 Z= 0.216 Angle : 0.602 13.678 54470 Z= 0.309 Chirality : 0.045 0.206 6071 Planarity : 0.005 0.063 6777 Dihedral : 11.978 168.804 5988 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.20 % Allowed : 13.04 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.12), residues: 4612 helix: 0.69 (0.12), residues: 1849 sheet: -0.56 (0.19), residues: 651 loop : -0.34 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 904 TYR 0.019 0.002 TYR D 109 PHE 0.030 0.002 PHE A 112 TRP 0.016 0.002 TRP B 104 HIS 0.005 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00504 (40067) covalent geometry : angle 0.59373 (54425) hydrogen bonds : bond 0.04015 ( 1714) hydrogen bonds : angle 4.86847 ( 4795) metal coordination : bond 0.00678 ( 32) metal coordination : angle 3.47048 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 492 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 TRP cc_start: 0.6551 (m-90) cc_final: 0.6297 (m-90) REVERT: A 248 MET cc_start: 0.8788 (mtt) cc_final: 0.8585 (mtm) REVERT: A 330 GLN cc_start: 0.7427 (tp40) cc_final: 0.6706 (tm-30) REVERT: A 637 MET cc_start: 0.9274 (ptp) cc_final: 0.8965 (ptp) REVERT: A 757 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: A 1034 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.6777 (tp40) REVERT: A 1153 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7804 (mtm180) REVERT: A 1227 THR cc_start: 0.8772 (t) cc_final: 0.8448 (p) REVERT: A 1234 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8196 (mttm) REVERT: A 1236 ASN cc_start: 0.8452 (m-40) cc_final: 0.7918 (t0) REVERT: A 1284 PHE cc_start: 0.7951 (t80) cc_final: 0.7456 (t80) REVERT: A 1285 LEU cc_start: 0.8417 (tp) cc_final: 0.8199 (mp) REVERT: A 1303 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7296 (mp10) REVERT: A 1325 ASP cc_start: 0.8416 (m-30) cc_final: 0.8109 (t0) REVERT: A 1421 ARG cc_start: 0.8449 (mmt90) cc_final: 0.8033 (mmp-170) REVERT: B 375 MET cc_start: 0.8215 (mmm) cc_final: 0.8003 (mmt) REVERT: B 495 TYR cc_start: 0.7352 (t80) cc_final: 0.7037 (t80) REVERT: B 515 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7718 (mtm110) REVERT: B 762 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7578 (ttmt) REVERT: B 972 PHE cc_start: 0.8709 (m-80) cc_final: 0.8483 (m-80) REVERT: B 1235 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8845 (tp) REVERT: E 193 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8766 (mp) REVERT: G 117 MET cc_start: 0.8105 (mmt) cc_final: 0.7652 (mmt) REVERT: H 4 ILE cc_start: 0.9167 (mm) cc_final: 0.8925 (mm) REVERT: H 66 GLU cc_start: 0.7668 (mp0) cc_final: 0.7284 (mp0) REVERT: H 133 HIS cc_start: 0.8154 (m-70) cc_final: 0.7913 (m-70) REVERT: I 47 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7927 (mm-30) REVERT: K 93 ASP cc_start: 0.8463 (m-30) cc_final: 0.8131 (m-30) REVERT: L 52 LEU cc_start: 0.8639 (mt) cc_final: 0.8388 (mp) REVERT: S 1287 MET cc_start: 0.4792 (tmm) cc_final: 0.4517 (tmm) outliers start: 91 outliers final: 71 residues processed: 554 average time/residue: 0.2578 time to fit residues: 229.7722 Evaluate side-chains 548 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 472 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain S residue 300 LEU Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 389 HIS Chi-restraints excluded: chain S residue 396 VAL Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain S residue 454 VAL Chi-restraints excluded: chain S residue 569 LEU Chi-restraints excluded: chain S residue 591 MET Chi-restraints excluded: chain S residue 592 VAL Chi-restraints excluded: chain S residue 721 LEU Chi-restraints excluded: chain S residue 747 ARG Chi-restraints excluded: chain S residue 782 LEU Chi-restraints excluded: chain S residue 792 HIS Chi-restraints excluded: chain S residue 899 SER Chi-restraints excluded: chain S residue 915 SER Chi-restraints excluded: chain S residue 934 ASP Chi-restraints excluded: chain S residue 1120 HIS Chi-restraints excluded: chain S residue 1156 GLU Chi-restraints excluded: chain S residue 1236 VAL Chi-restraints excluded: chain S residue 1257 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 187 optimal weight: 1.9990 chunk 359 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 331 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 453 optimal weight: 0.6980 chunk 151 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 437 optimal weight: 0.6980 chunk 325 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN J 61 ASN ** S 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 731 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.162807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131434 restraints weight = 68460.005| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.12 r_work: 0.3370 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40099 Z= 0.162 Angle : 0.573 13.545 54470 Z= 0.293 Chirality : 0.043 0.194 6071 Planarity : 0.004 0.061 6777 Dihedral : 11.934 169.509 5988 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.00 % Allowed : 13.41 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.12 (0.12), residues: 4612 helix: 0.83 (0.12), residues: 1849 sheet: -0.52 (0.19), residues: 649 loop : -0.26 (0.14), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 904 TYR 0.016 0.001 TYR I 37 PHE 0.029 0.001 PHE A 112 TRP 0.015 0.001 TRP B 104 HIS 0.006 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00377 (40067) covalent geometry : angle 0.56505 (54425) hydrogen bonds : bond 0.03751 ( 1714) hydrogen bonds : angle 4.78636 ( 4795) metal coordination : bond 0.00537 ( 32) metal coordination : angle 3.31069 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 489 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 TRP cc_start: 0.6460 (m-90) cc_final: 0.6240 (m-90) REVERT: A 231 GLU cc_start: 0.7726 (pm20) cc_final: 0.7445 (pm20) REVERT: A 330 GLN cc_start: 0.7389 (tp40) cc_final: 0.6666 (tm-30) REVERT: A 637 MET cc_start: 0.9263 (ptp) cc_final: 0.8949 (ptp) REVERT: A 757 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: A 921 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8621 (ttt90) REVERT: A 1034 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.6719 (tp40) REVERT: A 1227 THR cc_start: 0.8851 (t) cc_final: 0.8517 (p) REVERT: A 1234 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8283 (mttm) REVERT: A 1236 ASN cc_start: 0.8446 (m-40) cc_final: 0.7911 (t0) REVERT: A 1262 MET cc_start: 0.5840 (mmp) cc_final: 0.5439 (mmm) REVERT: A 1285 LEU cc_start: 0.8467 (tp) cc_final: 0.8255 (mp) REVERT: A 1292 MET cc_start: 0.8423 (mtm) cc_final: 0.8197 (mtm) REVERT: A 1303 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7331 (mp10) REVERT: A 1325 ASP cc_start: 0.8407 (m-30) cc_final: 0.8096 (t0) REVERT: A 1421 ARG cc_start: 0.8452 (mmt90) cc_final: 0.8006 (mmp-170) REVERT: B 343 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: B 375 MET cc_start: 0.8175 (mmm) cc_final: 0.7962 (mmt) REVERT: B 495 TYR cc_start: 0.7274 (t80) cc_final: 0.6963 (t80) REVERT: B 515 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7694 (mtm110) REVERT: B 672 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: B 762 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7598 (ttmt) REVERT: B 972 PHE cc_start: 0.8661 (m-80) cc_final: 0.8435 (m-80) REVERT: B 1235 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8692 (tp) REVERT: E 18 MET cc_start: 0.9155 (mmp) cc_final: 0.8852 (mmp) REVERT: E 193 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8767 (mp) REVERT: G 117 MET cc_start: 0.8095 (mmt) cc_final: 0.7626 (mmt) REVERT: H 4 ILE cc_start: 0.9138 (mm) cc_final: 0.8906 (mm) REVERT: H 66 GLU cc_start: 0.7672 (mp0) cc_final: 0.7282 (mp0) REVERT: H 133 HIS cc_start: 0.8151 (m-70) cc_final: 0.7898 (m-70) REVERT: I 47 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7928 (mm-30) REVERT: K 93 ASP cc_start: 0.8453 (m-30) cc_final: 0.8136 (m-30) REVERT: L 52 LEU cc_start: 0.8638 (mt) cc_final: 0.8402 (mp) outliers start: 83 outliers final: 69 residues processed: 543 average time/residue: 0.2773 time to fit residues: 240.8827 Evaluate side-chains 549 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 472 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 389 HIS Chi-restraints excluded: chain S residue 396 VAL Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain S residue 454 VAL Chi-restraints excluded: chain S residue 569 LEU Chi-restraints excluded: chain S residue 591 MET Chi-restraints excluded: chain S residue 592 VAL Chi-restraints excluded: chain S residue 721 LEU Chi-restraints excluded: chain S residue 747 ARG Chi-restraints excluded: chain S residue 782 LEU Chi-restraints excluded: chain S residue 792 HIS Chi-restraints excluded: chain S residue 899 SER Chi-restraints excluded: chain S residue 915 SER Chi-restraints excluded: chain S residue 934 ASP Chi-restraints excluded: chain S residue 1120 HIS Chi-restraints excluded: chain S residue 1156 GLU Chi-restraints excluded: chain S residue 1236 VAL Chi-restraints excluded: chain S residue 1257 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 40 optimal weight: 8.9990 chunk 372 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 465 optimal weight: 0.0870 chunk 308 optimal weight: 0.9990 chunk 336 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** S 561 GLN ** 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 = 0.4011 r_free = 0.4011 target = 0.163436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131850 restraints weight = 67955.722| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.21 r_work: 0.3370 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40099 Z= 0.144 Angle : 0.565 13.304 54470 Z= 0.289 Chirality : 0.043 0.189 6071 Planarity : 0.004 0.060 6777 Dihedral : 11.885 169.602 5988 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.81 % Allowed : 13.86 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.20 (0.12), residues: 4612 helix: 0.89 (0.12), residues: 1854 sheet: -0.47 (0.19), residues: 651 loop : -0.23 (0.14), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 904 TYR 0.016 0.001 TYR I 37 PHE 0.029 0.001 PHE A 112 TRP 0.016 0.001 TRP A 479 HIS 0.006 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00334 (40067) covalent geometry : angle 0.55817 (54425) hydrogen bonds : bond 0.03607 ( 1714) hydrogen bonds : angle 4.71081 ( 4795) metal coordination : bond 0.00451 ( 32) metal coordination : angle 3.12176 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 498 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TRP cc_start: 0.6429 (m-90) cc_final: 0.6186 (m-90) REVERT: A 232 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 327 ARG cc_start: 0.8088 (mmt90) cc_final: 0.7721 (mmt-90) REVERT: A 330 GLN cc_start: 0.7463 (tp40) cc_final: 0.6889 (tm-30) REVERT: A 637 MET cc_start: 0.9272 (ptp) cc_final: 0.8944 (ptp) REVERT: A 921 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8884 (ttp80) REVERT: A 1034 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.6786 (tp40) REVERT: A 1227 THR cc_start: 0.8851 (t) cc_final: 0.8514 (p) REVERT: A 1236 ASN cc_start: 0.8473 (m-40) cc_final: 0.7901 (t0) REVERT: A 1262 MET cc_start: 0.5905 (mmp) cc_final: 0.5533 (mmm) REVERT: A 1284 PHE cc_start: 0.8108 (t80) cc_final: 0.7845 (t80) REVERT: A 1285 LEU cc_start: 0.8473 (tp) cc_final: 0.8270 (mp) REVERT: A 1303 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7364 (mp10) REVERT: A 1421 ARG cc_start: 0.8429 (mmt90) cc_final: 0.7995 (mmp-170) REVERT: B 343 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: B 375 MET cc_start: 0.8206 (mmm) cc_final: 0.7980 (mmt) REVERT: B 495 TYR cc_start: 0.7276 (t80) cc_final: 0.6984 (t80) REVERT: B 515 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7713 (mtm110) REVERT: B 658 GLU cc_start: 0.8370 (tt0) cc_final: 0.8020 (pm20) REVERT: B 672 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: B 762 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7503 (ttmt) REVERT: B 1235 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8705 (tp) REVERT: C 130 VAL cc_start: 0.9252 (t) cc_final: 0.8904 (m) REVERT: E 70 ASP cc_start: 0.7688 (t0) cc_final: 0.7200 (t70) REVERT: E 168 ASN cc_start: 0.9187 (p0) cc_final: 0.8961 (p0) REVERT: F 80 MET cc_start: 0.9066 (mmp) cc_final: 0.8815 (mmp) REVERT: G 117 MET cc_start: 0.8080 (mmt) cc_final: 0.7633 (mmt) REVERT: H 4 ILE cc_start: 0.9109 (mm) cc_final: 0.8877 (mm) REVERT: H 66 GLU cc_start: 0.7671 (mp0) cc_final: 0.7363 (mp0) REVERT: H 133 HIS cc_start: 0.8184 (m-70) cc_final: 0.7944 (m-70) REVERT: I 47 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7924 (mm-30) REVERT: K 93 ASP cc_start: 0.8488 (m-30) cc_final: 0.8150 (m-30) REVERT: L 52 LEU cc_start: 0.8624 (mt) cc_final: 0.8391 (mp) outliers start: 75 outliers final: 58 residues processed: 546 average time/residue: 0.2771 time to fit residues: 241.8907 Evaluate side-chains 543 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 479 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 389 HIS Chi-restraints excluded: chain S residue 443 LEU Chi-restraints excluded: chain S residue 591 MET Chi-restraints excluded: chain S residue 747 ARG Chi-restraints excluded: chain S residue 792 HIS Chi-restraints excluded: chain S residue 915 SER Chi-restraints excluded: chain S residue 934 ASP Chi-restraints excluded: chain S residue 1120 HIS Chi-restraints excluded: chain S residue 1156 GLU Chi-restraints excluded: chain S residue 1236 VAL Chi-restraints excluded: chain S residue 1257 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 359 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 402 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 265 optimal weight: 0.5980 chunk 446 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** S 561 GLN ** 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 = 0.4010 r_free = 0.4010 target = 0.163276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131682 restraints weight = 68746.962| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.19 r_work: 0.3376 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 40099 Z= 0.184 Angle : 0.655 59.199 54470 Z= 0.358 Chirality : 0.045 0.902 6071 Planarity : 0.004 0.059 6777 Dihedral : 11.886 169.626 5988 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.74 % Allowed : 13.84 % Favored : 84.42 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.40 % 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: 0.19 (0.12), residues: 4612 helix: 0.88 (0.12), residues: 1855 sheet: -0.46 (0.19), residues: 651 loop : -0.24 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 904 TYR 0.015 0.001 TYR I 37 PHE 0.034 0.002 PHE S1161 TRP 0.015 0.001 TRP B 104 HIS 0.006 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00420 (40067) covalent geometry : angle 0.64963 (54425) hydrogen bonds : bond 0.03679 ( 1714) hydrogen bonds : angle 4.71387 ( 4795) metal coordination : bond 0.00745 ( 32) metal coordination : angle 3.09336 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12204.74 seconds wall clock time: 209 minutes 7.26 seconds (12547.26 seconds total)