Starting phenix.real_space_refine on Tue Sep 15 16:20:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5fyw_3378/09_2026/5fyw_3378.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fyw_3378/09_2026/5fyw_3378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5fyw_3378/09_2026/5fyw_3378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fyw_3378/09_2026/5fyw_3378.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5fyw_3378/09_2026/5fyw_3378.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5fyw_3378/09_2026/5fyw_3378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5fyw_3378/09_2026/5fyw_3378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fyw_3378/09_2026/5fyw_3378.map" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 10 6.06 5 P 92 5.49 5 Mg 1 5.21 5 S 218 5.16 5 C 26079 2.51 5 N 7325 2.21 5 O 7985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41710 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 10997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10997 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 9203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9203 Classifications: {'peptide': 1157} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 51, 'TRANS': 1105} Chain breaks: 8 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2061 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1785 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 919 Inner-chain residues flagged as termini: ['pdbres=" DG N 60 "'] Classifications: {'DNA': 47} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 46} Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 46 Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "Q" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1144 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 9, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1347 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 6, 'HIS:plan': 2, 'GLU:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 178 Chain: "T" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 909 Classifications: {'DNA': 47} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 46} Chain breaks: 1 Unresolved chain link angles: 46 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 46 Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 757 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'TRANS': 91} Chain breaks: 1 Chain: "V" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 782 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain breaks: 1 Chain: "W" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 835 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 727 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASP:plan': 15, 'ASN:plan1': 5, 'PHE:plan': 6, 'ARG:plan': 9, 'TYR:plan': 8, 'HIS:plan': 4, 'GLU:plan': 8, 'GLN:plan1': 9, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 294 Chain: "X" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 710 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 506 Unresolved non-hydrogen angles: 639 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 13, 'TRP:plan': 4, 'GLU:plan': 12, 'TYR:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 4, 'ARG:plan': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 253 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" 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 813 SG CYS A 107 89.951 126.607 127.521 1.00164.06 S ATOM 837 SG CYS A 110 88.961 128.300 130.243 1.00142.57 S ATOM 1142 SG CYS A 148 92.379 129.765 129.479 1.00179.23 S ATOM 508 SG CYS A 67 48.316 120.643 103.771 1.00107.66 S ATOM 530 SG CYS A 70 48.235 124.884 105.496 1.00105.81 S ATOM 583 SG CYS A 77 49.838 123.276 102.328 1.00116.68 S ATOM 19718 SG CYS B1163 54.738 135.381 114.308 1.00110.90 S ATOM 19736 SG CYS B1166 57.488 132.890 113.966 1.00118.04 S ATOM 19861 SG CYS B1182 54.272 131.067 113.537 1.00120.54 S ATOM 19880 SG CYS B1185 54.880 132.742 116.277 1.00120.04 S ATOM 20847 SG CYS C 86 25.902 125.803 39.755 1.00132.68 S ATOM 20864 SG CYS C 88 26.454 123.091 41.843 1.00140.95 S ATOM 20897 SG CYS C 92 26.596 122.609 38.399 1.00 94.59 S ATOM 20920 SG CYS C 95 29.612 123.984 39.639 1.00 92.85 S ATOM 28410 SG CYS I 7 141.093 106.199 87.944 1.00191.60 S ATOM 28435 SG CYS I 10 138.997 103.830 90.156 1.00209.03 S ATOM 28601 SG CYS I 29 138.587 108.127 90.178 1.00219.81 S ATOM 28625 SG CYS I 32 141.292 105.940 91.471 1.00210.19 S ATOM 28952 SG CYS I 75 134.291 125.025 48.007 1.00167.19 S ATOM 28974 SG CYS I 78 134.853 122.022 45.382 1.00183.43 S ATOM 29190 SG CYS I 103 131.634 121.540 46.749 1.00183.79 S ATOM 29210 SG CYS I 106 134.981 121.362 48.753 1.00188.57 S ATOM 29355 SG CYS J 7 60.577 126.549 33.058 1.00 72.78 S ATOM 29378 SG CYS J 10 59.304 128.837 30.709 1.00 59.38 S ATOM 29658 SG CYS J 45 62.351 130.189 30.592 1.00 71.52 S ATOM 29664 SG CYS J 46 60.948 126.900 28.666 1.00 97.89 S ATOM 30787 SG CYS L 31 54.243 89.117 54.837 1.00150.62 S ATOM 30807 SG CYS L 34 53.518 87.028 52.168 1.00133.37 S ATOM 30911 SG CYS L 48 52.247 86.723 56.174 1.00148.15 S ATOM 30934 SG CYS L 51 55.497 85.871 54.896 1.00145.50 S ATOM 31162 SG CYS M 24 29.267 126.335 87.350 1.00148.82 S ATOM 31184 SG CYS M 27 26.791 125.414 85.082 1.00150.84 S ATOM 31328 SG CYS M 45 29.953 123.670 83.894 1.00165.01 S ATOM 31347 SG CYS M 48 29.131 127.721 84.193 1.00115.83 S Time building chain proxies: 7.89, per 1000 atoms: 0.19 Number of scatterers: 41710 At special positions: 0 Unit cell: (164.7, 216, 167.4, 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 10 29.99 S 218 16.00 P 92 15.00 Mg 1 11.99 O 7985 8.00 N 7325 7.00 C 26079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2453 " pdb="ZN ZN A2453 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2453 " - pdb=" SG CYS A 148 " pdb="ZN ZN A2453 " - pdb=" SG CYS A 110 " pdb=" ZN A2454 " pdb="ZN ZN A2454 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2454 " - pdb=" SG CYS A 77 " pdb="ZN ZN A2454 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2454 " - pdb=" NE2 HIS A 80 " pdb=" ZN B2224 " pdb="ZN ZN B2224 " - pdb=" SG CYS B1182 " pdb="ZN ZN B2224 " - pdb=" SG CYS B1166 " pdb="ZN ZN B2224 " - pdb=" SG CYS B1185 " pdb="ZN ZN B2224 " - pdb=" SG CYS B1163 " pdb=" ZN C1266 " pdb="ZN ZN C1266 " - pdb=" SG CYS C 88 " pdb="ZN ZN C1266 " - pdb=" SG CYS C 92 " pdb="ZN ZN C1266 " - pdb=" SG CYS C 86 " pdb="ZN ZN C1266 " - pdb=" SG CYS C 95 " pdb=" ZN I1118 " pdb="ZN ZN I1118 " - pdb=" SG CYS I 7 " pdb="ZN ZN I1118 " - pdb=" SG CYS I 29 " pdb="ZN ZN I1118 " - pdb=" SG CYS I 32 " pdb="ZN ZN I1118 " - pdb=" SG CYS I 10 " pdb=" ZN I1119 " pdb="ZN ZN I1119 " - pdb=" SG CYS I 106 " pdb="ZN ZN I1119 " - pdb=" SG CYS I 78 " pdb="ZN ZN I1119 " - pdb=" SG CYS I 75 " pdb="ZN ZN I1119 " - pdb=" SG CYS I 103 " pdb=" ZN J1066 " pdb="ZN ZN J1066 " - pdb=" SG CYS J 10 " pdb="ZN ZN J1066 " - pdb=" SG CYS J 46 " pdb="ZN ZN J1066 " - pdb=" SG CYS J 45 " pdb="ZN ZN J1066 " - pdb=" SG CYS J 7 " pdb=" ZN L1071 " pdb="ZN ZN L1071 " - pdb=" SG CYS L 51 " pdb="ZN ZN L1071 " - pdb=" SG CYS L 34 " pdb="ZN ZN L1071 " - pdb=" SG CYS L 31 " pdb="ZN ZN L1071 " - pdb=" SG CYS L 48 " pdb=" ZN M1327 " pdb="ZN ZN M1327 " - pdb=" SG CYS M 48 " pdb="ZN ZN M1327 " - pdb=" SG CYS M 27 " pdb="ZN ZN M1327 " - pdb=" SG CYS M 45 " pdb="ZN ZN M1327 " - pdb=" SG CYS M 24 " Number of angles added : 45 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9778 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 81 sheets defined 42.0% alpha, 22.0% beta 38 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.676A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.062A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.644A pdb=" N ILE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 305 Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.361A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 4.218A pdb=" N MET A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.919A pdb=" N ALA A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.781A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.622A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.550A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.654A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.721A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.798A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 646 " --> pdb=" O CYS A 642 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.684A pdb=" N ALA A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.610A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.636A pdb=" N PHE A 815 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 912 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 922 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.795A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 removed outlier: 3.875A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1034 removed outlier: 5.345A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ARG A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG A1030 " --> pdb=" O LEU A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 4.004A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.877A pdb=" N ALA A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.737A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.696A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1255 through 1269 removed outlier: 4.408A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A1265 " --> pdb=" O LYS A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1319 removed outlier: 3.856A pdb=" N VAL A1316 " --> pdb=" O ASN A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1360 removed outlier: 3.683A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.969A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1403 removed outlier: 3.933A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1415 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1436 through 1441 removed outlier: 4.409A pdb=" N PHE A1441 " --> pdb=" O THR A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1452 removed outlier: 3.864A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.981A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 67 removed outlier: 3.775A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.576A pdb=" N SER B 182 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 324 removed outlier: 4.382A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.651A pdb=" N GLY B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.735A pdb=" N GLY B 342 " --> pdb=" O THR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 358 removed outlier: 3.988A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.668A pdb=" N PHE B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 464 removed outlier: 4.404A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 removed outlier: 3.786A pdb=" N SER B 559 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP B 561 " --> pdb=" O PHE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.775A pdb=" N THR B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.751A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.705A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 761 Processing helix chain 'B' and resid 763 through 777 removed outlier: 3.515A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 777 " --> pdb=" O MET B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 removed outlier: 4.540A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 813 removed outlier: 3.700A pdb=" N LYS B 813 " --> pdb=" O GLU B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 927 through 932 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.382A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1039 removed outlier: 3.640A pdb=" N CYS B1029 " --> pdb=" O HIS B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.624A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.601A pdb=" N LYS B1102 " --> pdb=" O MET B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 removed outlier: 3.719A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.608A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.704A pdb=" N GLU C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 239 through 264 Processing helix chain 'D' and resid 53 through 73 removed outlier: 3.618A pdb=" N ILE D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.720A pdb=" N LEU D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.830A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.799A pdb=" N ALA D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.521A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.650A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.553A pdb=" N ILE D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 37 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.784A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.805A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 16 through 29 removed outlier: 4.251A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.763A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 53 removed outlier: 4.068A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.683A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.217A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.825A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 140 Processing helix chain 'M' and resid 143 through 158 Processing helix chain 'M' and resid 168 through 183 removed outlier: 3.615A pdb=" N MET M 172 " --> pdb=" O MET M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 196 Processing helix chain 'M' and resid 200 through 217 Processing helix chain 'M' and resid 237 through 247 removed outlier: 3.843A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 267 Processing helix chain 'M' and resid 273 through 289 removed outlier: 3.968A pdb=" N ILE M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 305 through 319 removed outlier: 3.680A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 324 removed outlier: 3.613A pdb=" N LEU M 323 " --> pdb=" O ARG M 320 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL M 324 " --> pdb=" O ASP M 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 320 through 324' Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 147 Processing helix chain 'O' and resid 171 through 179 Processing helix chain 'O' and resid 219 through 237 removed outlier: 3.849A pdb=" N ILE O 223 " --> pdb=" O GLN O 219 " (cutoff:3.500A) Proline residue: O 232 - end of helix Processing helix chain 'Q' and resid 26 through 35 Processing helix chain 'Q' and resid 107 through 114 removed outlier: 4.051A pdb=" N LEU Q 111 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 337 through 346 Processing helix chain 'Q' and resid 405 through 414 Processing helix chain 'R' and resid 74 through 82 Processing helix chain 'R' and resid 233 through 244 removed outlier: 3.923A pdb=" N VAL R 237 " --> pdb=" O TYR R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 295 through 310 Processing helix chain 'R' and resid 314 through 323 Processing helix chain 'R' and resid 325 through 336 removed outlier: 3.616A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 370 Processing helix chain 'U' and resid 3 through 28 removed outlier: 4.043A pdb=" N SER U 7 " --> pdb=" O ASN U 3 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 47 Processing helix chain 'V' and resid 8 through 12 Processing helix chain 'V' and resid 13 through 29 Processing helix chain 'V' and resid 35 through 55 Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 22 through 35 removed outlier: 3.719A pdb=" N VAL W 26 " --> pdb=" O GLY W 22 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 47 Processing helix chain 'W' and resid 50 through 64 Proline residue: W 56 - end of helix removed outlier: 3.615A pdb=" N ASP W 64 " --> pdb=" O ARG W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 90 through 111 removed outlier: 3.546A pdb=" N ALA W 94 " --> pdb=" O LYS W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 140 Processing helix chain 'W' and resid 168 through 191 Proline residue: W 181 - end of helix Processing helix chain 'X' and resid 124 through 139 removed outlier: 4.359A pdb=" N LEU X 128 " --> pdb=" O ASP X 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU X 129 " --> pdb=" O SER X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 151 Processing helix chain 'X' and resid 156 through 166 removed outlier: 4.184A pdb=" N ILE X 160 " --> pdb=" O ASP X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 199 Processing helix chain 'X' and resid 200 through 202 No H-bonds generated for 'chain 'X' and resid 200 through 202' Processing helix chain 'X' and resid 206 through 214 Processing helix chain 'X' and resid 216 through 228 removed outlier: 4.428A pdb=" N THR X 220 " --> pdb=" O GLN X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 263 Processing helix chain 'X' and resid 272 through 280 Processing sheet with id=AA, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AB, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.072A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.759A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AE, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AF, first strand: chain 'A' and resid 455 through 456 removed outlier: 4.069A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'A' and resid 455 through 456 removed outlier: 4.069A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AI, first strand: chain 'A' and resid 363 through 367 Processing sheet with id=AJ, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.751A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.702A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AM, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.485A pdb=" N TYR H 102 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N SER H 117 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE H 104 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N TYR H 115 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU H 106 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA H 113 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.734A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AO, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AP, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AQ, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.544A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AR, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AS, first strand: chain 'A' and resid 1280 through 1287 removed outlier: 5.447A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP A1309 " --> pdb=" O ARG A1281 " (cutoff:3.500A) Processing sheet with id=AT, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.883A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER A1150 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG I 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A1152 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AU, first strand: chain 'A' and resid 1290 through 1292 Processing sheet with id=AV, first strand: chain 'A' and resid 1442 through 1444 Processing sheet with id=BA, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=BB, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.675A pdb=" N TYR B 149 " --> pdb=" O GLU B 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=BB Processing sheet with id=BC, first strand: chain 'B' and resid 164 through 171 removed outlier: 5.926A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=QA, first strand: chain 'Q' and resid 331 through 333 removed outlier: 4.051A pdb=" N LYS Q 333 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE B 70 " --> pdb=" O LYS Q 333 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N HIS B 110 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing sheet with id=QB, first strand: chain 'Q' and resid 331 through 333 removed outlier: 4.051A pdb=" N LYS Q 333 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE B 70 " --> pdb=" O LYS Q 333 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU B 89 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N TYR B 137 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER B 91 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ARG B 135 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY B 93 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N LYS B 133 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 95 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP B 131 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL B 97 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE B 129 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS B 99 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY B 127 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER B 125 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR B 149 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=BE, first strand: chain 'B' and resid 215 through 218 Processing sheet with id=BF, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.752A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=BG, first strand: chain 'B' and resid 497 through 499 Processing sheet with id=BH, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=BI, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=BJ, first strand: chain 'B' and resid 690 through 694 Processing sheet with id=BK, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=BL, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=BM, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.114A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=BN, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.515A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=BO, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.515A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=BP, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=BQ, first strand: chain 'B' and resid 987 through 989 Processing sheet with id=BR, first strand: chain 'B' and resid 987 through 989 removed outlier: 4.149A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=BS, first strand: chain 'B' and resid 1069 through 1070 Processing sheet with id=BT, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=BU, first strand: chain 'B' and resid 910 through 912 removed outlier: 6.880A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) Processing sheet with id=BV, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=BW, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=BX, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=CA, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.716A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.139A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.814A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=DB, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.631A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=DC, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.631A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 60 through 61 Processing sheet with id=EA, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.668A pdb=" N TRP E 79 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=EC, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.577A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=GB, first strand: chain 'G' and resid 85 through 95 removed outlier: 5.728A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) Processing sheet with id=GC, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=IA, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=IB, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.635A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=KA, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.565A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=MA, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.328A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=OA, first strand: chain 'O' and resid 92 through 93 removed outlier: 3.586A pdb=" N ILE O 106 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL O 122 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL O 74 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N THR O 124 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA O 72 " --> pdb=" O THR O 124 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA O 126 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU O 67 " --> pdb=" O VAL O 161 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL O 161 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN O 69 " --> pdb=" O ASN O 159 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN O 159 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL O 71 " --> pdb=" O ILE O 157 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE O 157 " --> pdb=" O VAL O 71 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR O 73 " --> pdb=" O PHE O 155 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE O 155 " --> pdb=" O THR O 73 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE O 160 " --> pdb=" O GLY O 216 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY O 216 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing sheet with id=QC, first strand: chain 'Q' and resid 98 through 105 removed outlier: 4.569A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 119 through 126 current: chain 'R' and resid 133 through 138 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 133 through 138 current: chain 'R' and resid 220 through 225 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 220 through 225 current: chain 'R' and resid 64 through 72 removed outlier: 4.386A pdb=" N GLN R 67 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 384 through 388 current: chain 'Q' and resid 391 through 398 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 391 through 398 current: chain 'Q' and resid 138 through 141 Processing sheet with id=151, first strand: chain 'Q' and resid 393 through 398 No H-bonds generated for sheet with id=151 Processing sheet with id=144, first strand: chain 'Q' and resid 115 through 121 No H-bonds generated for sheet with id=144 Processing sheet with id=145, first strand: chain 'Q' and resid 138 through 141 No H-bonds generated for sheet with id=145 Processing sheet with id=147, first strand: chain 'Q' and resid 350 through 353 No H-bonds generated for sheet with id=147 Processing sheet with id=148, first strand: chain 'Q' and resid 360 through 365 No H-bonds generated for sheet with id=148 Processing sheet with id=RA, first strand: chain 'R' and resid 338 through 340 Processing sheet with id=156, first strand: chain 'R' and resid 133 through 138 No H-bonds generated for sheet with id=156 Processing sheet with id=157, first strand: chain 'R' and resid 211 through 218 No H-bonds generated for sheet with id=157 Processing sheet with id=158, first strand: chain 'R' and resid 220 through 225 No H-bonds generated for sheet with id=158 Processing sheet with id=159, first strand: chain 'R' and resid 253 through 255 No H-bonds generated for sheet with id=159 Processing sheet with id=UA, first strand: chain 'U' and resid 243 through 254 removed outlier: 6.967A pdb=" N VAL V 105 " --> pdb=" O THR V 86 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR V 86 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER V 107 " --> pdb=" O GLN V 84 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN V 84 " --> pdb=" O SER V 107 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP V 109 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP V 76 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE V 71 " --> pdb=" O TRP V 76 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE V 78 " --> pdb=" O TYR V 69 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR V 69 " --> pdb=" O PHE V 78 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL V 80 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP V 67 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN V 82 " --> pdb=" O ASN V 65 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN V 65 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP U 273 " --> pdb=" O THR U 268 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR U 268 " --> pdb=" O ASP U 273 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR U 275 " --> pdb=" O VAL U 266 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL U 266 " --> pdb=" O THR U 275 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLN U 277 " --> pdb=" O ASP U 264 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP U 258 " --> pdb=" O ARG U 253 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG U 253 " --> pdb=" O TRP U 258 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS U 260 " --> pdb=" O VAL U 251 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL U 251 " --> pdb=" O CYS U 260 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU U 262 " --> pdb=" O ASP U 249 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP U 249 " --> pdb=" O LEU U 262 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP U 264 " --> pdb=" O LEU U 247 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU U 247 " --> pdb=" O ASP U 264 " (cutoff:3.500A) Processing sheet with id=WA, first strand: chain 'W' and resid 68 through 74 Processing sheet with id=WB, first strand: chain 'W' and resid 122 through 123 Processing sheet with id=XA, first strand: chain 'X' and resid 169 through 171 Processing sheet with id=XB, first strand: chain 'X' and resid 232 through 234 1894 hydrogen bonds defined for protein. 5253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 12.98 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 1 1.20 - 1.36: 14003 1.36 - 1.52: 19846 1.52 - 1.68: 8387 1.68 - 1.84: 345 Bond restraints: 42582 Sorted by residual: bond pdb=" C ASN H 131 " pdb=" N LEU H 132 " ideal model delta sigma weight residual 1.332 1.035 0.297 1.40e-02 5.10e+03 4.50e+02 bond pdb=" P DA T 53 " pdb=" O5' DA T 53 " ideal model delta sigma weight residual 1.593 1.478 0.115 1.00e-02 1.00e+04 1.32e+02 bond pdb=" C1' DA T 47 " pdb=" N9 DA T 47 " ideal model delta sigma weight residual 1.468 1.324 0.144 1.40e-02 5.10e+03 1.06e+02 bond pdb=" C1' DC T 64 " pdb=" N1 DC T 64 " ideal model delta sigma weight residual 1.468 1.569 -0.101 1.40e-02 5.10e+03 5.22e+01 bond pdb=" C1' DC T 61 " pdb=" N1 DC T 61 " ideal model delta sigma weight residual 1.468 1.568 -0.100 1.40e-02 5.10e+03 5.09e+01 ... (remaining 42577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.77: 57751 8.77 - 17.55: 35 17.55 - 26.32: 3 26.32 - 35.10: 0 35.10 - 43.87: 2 Bond angle restraints: 57791 Sorted by residual: angle pdb=" C ASN H 131 " pdb=" N LEU H 132 " pdb=" CA LEU H 132 " ideal model delta sigma weight residual 121.54 160.91 -39.37 1.91e+00 2.74e-01 4.25e+02 angle pdb=" N ASN H 131 " pdb=" CA ASN H 131 " pdb=" C ASN H 131 " ideal model delta sigma weight residual 110.80 154.67 -43.87 2.13e+00 2.20e-01 4.24e+02 angle pdb=" O ASN H 131 " pdb=" C ASN H 131 " pdb=" N LEU H 132 " ideal model delta sigma weight residual 122.59 97.34 25.25 1.33e+00 5.65e-01 3.60e+02 angle pdb=" CA ASN H 131 " pdb=" C ASN H 131 " pdb=" N LEU H 132 " ideal model delta sigma weight residual 116.84 138.63 -21.79 1.71e+00 3.42e-01 1.62e+02 angle pdb=" C VAL R 336 " pdb=" CA VAL R 336 " pdb=" CB VAL R 336 " ideal model delta sigma weight residual 111.29 90.60 20.69 1.64e+00 3.72e-01 1.59e+02 ... (remaining 57786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.98: 24516 20.98 - 41.97: 926 41.97 - 62.95: 331 62.95 - 83.94: 27 83.94 - 104.92: 6 Dihedral angle restraints: 25806 sinusoidal: 10763 harmonic: 15043 Sorted by residual: dihedral pdb=" CA ASN H 131 " pdb=" C ASN H 131 " pdb=" N LEU H 132 " pdb=" CA LEU H 132 " ideal model delta harmonic sigma weight residual -180.00 -121.77 -58.23 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" C VAL R 336 " pdb=" N VAL R 336 " pdb=" CA VAL R 336 " pdb=" CB VAL R 336 " ideal model delta harmonic sigma weight residual -122.00 -93.70 -28.30 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" CA LEU B1175 " pdb=" C LEU B1175 " pdb=" N ASN B1176 " pdb=" CA ASN B1176 " ideal model delta harmonic sigma weight residual 180.00 123.54 56.46 0 5.00e+00 4.00e-02 1.28e+02 ... (remaining 25803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 6536 0.277 - 0.554: 20 0.554 - 0.831: 1 0.831 - 1.108: 1 1.108 - 1.385: 1 Chirality restraints: 6559 Sorted by residual: chirality pdb=" CA ASN H 131 " pdb=" N ASN H 131 " pdb=" C ASN H 131 " pdb=" CB ASN H 131 " both_signs ideal model delta sigma weight residual False 2.51 1.13 1.39 2.00e-01 2.50e+01 4.80e+01 chirality pdb=" CA VAL R 336 " pdb=" N VAL R 336 " pdb=" C VAL R 336 " pdb=" CB VAL R 336 " both_signs ideal model delta sigma weight residual False 2.44 3.28 -0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" C1' DC T 52 " pdb=" O4' DC T 52 " pdb=" C2' DC T 52 " pdb=" N1 DC T 52 " both_signs ideal model delta sigma weight residual False 2.43 1.87 0.56 2.00e-01 2.50e+01 7.96e+00 ... (remaining 6556 not shown) Planarity restraints: 7176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N 67 " -0.089 2.00e-02 2.50e+03 6.06e-02 9.19e+01 pdb=" N1 DT N 67 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT N 67 " 0.015 2.00e-02 2.50e+03 pdb=" O2 DT N 67 " 0.070 2.00e-02 2.50e+03 pdb=" N3 DT N 67 " 0.035 2.00e-02 2.50e+03 pdb=" C4 DT N 67 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT N 67 " -0.121 2.00e-02 2.50e+03 pdb=" C5 DT N 67 " 0.069 2.00e-02 2.50e+03 pdb=" C7 DT N 67 " 0.047 2.00e-02 2.50e+03 pdb=" C6 DT N 67 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 45 " 0.057 2.00e-02 2.50e+03 5.29e-02 6.98e+01 pdb=" N1 DT T 45 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT T 45 " -0.019 2.00e-02 2.50e+03 pdb=" O2 DT T 45 " -0.074 2.00e-02 2.50e+03 pdb=" N3 DT T 45 " -0.029 2.00e-02 2.50e+03 pdb=" C4 DT T 45 " 0.035 2.00e-02 2.50e+03 pdb=" O4 DT T 45 " 0.073 2.00e-02 2.50e+03 pdb=" C5 DT T 45 " 0.019 2.00e-02 2.50e+03 pdb=" C7 DT T 45 " -0.102 2.00e-02 2.50e+03 pdb=" C6 DT T 45 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 20 " -0.062 2.00e-02 2.50e+03 4.92e-02 6.06e+01 pdb=" N1 DT N 20 " 0.019 2.00e-02 2.50e+03 pdb=" C2 DT N 20 " 0.019 2.00e-02 2.50e+03 pdb=" O2 DT N 20 " -0.041 2.00e-02 2.50e+03 pdb=" N3 DT N 20 " 0.070 2.00e-02 2.50e+03 pdb=" C4 DT N 20 " 0.016 2.00e-02 2.50e+03 pdb=" O4 DT N 20 " -0.071 2.00e-02 2.50e+03 pdb=" C5 DT N 20 " 0.052 2.00e-02 2.50e+03 pdb=" C7 DT N 20 " -0.050 2.00e-02 2.50e+03 pdb=" C6 DT N 20 " 0.049 2.00e-02 2.50e+03 ... (remaining 7173 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 15 1.80 - 2.57: 439 2.57 - 3.35: 54202 3.35 - 4.12: 99600 4.12 - 4.90: 183392 Nonbonded interactions: 337648 Sorted by model distance: nonbonded pdb=" O GLY B 867 " pdb=" OE1 GLU M 152 " model vdw 1.021 3.040 nonbonded pdb=" NE2 GLN D 37 " pdb=" NZ LYS G 5 " model vdw 1.244 3.200 nonbonded pdb=" OE2 GLU B 104 " pdb=" NH1 ARG L 54 " model vdw 1.277 3.120 nonbonded pdb=" OD1 ASN O 95 " pdb=" CE2 PHE V 71 " model vdw 1.457 3.340 nonbonded pdb=" OE1 GLU B 104 " pdb=" NH2 ARG L 54 " model vdw 1.535 3.120 ... (remaining 337643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 49.100 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 : 0.012 1.185 42618 Z= 0.801 Angle : 1.222 43.874 57836 Z= 0.722 Chirality : 0.067 1.385 6559 Planarity : 0.007 0.107 7176 Dihedral : 12.925 104.923 16028 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.37 % Favored : 94.10 % Rotamer: Outliers : 0.77 % Allowed : 1.84 % Favored : 97.39 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.10), residues: 5066 helix: -2.27 (0.10), residues: 1891 sheet: -1.45 (0.15), residues: 910 loop : -1.54 (0.11), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG O 220 TYR 0.072 0.004 TYR U 274 PHE 0.057 0.004 PHE O 190 TRP 0.068 0.005 TRP B 586 HIS 0.016 0.003 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00976 / 0.54 (42582) covalent geometry : angle 1.13538 / 0.72 (57791) hydrogen bonds : bond 0.15681 / 10.95 ( 1919) hydrogen bonds : angle 9.00816 / 6.39 ( 5437) metal coordination : bond 0.17306 / 12.75 ( 35) metal coordination : angle 16.20692 / 11.41 ( 45) Misc. bond : bond 1.18450 / 74.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1064 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ARG cc_start: 0.9304 (ttt-90) cc_final: 0.8791 (ttp80) REVERT: A 330 LYS cc_start: 0.9238 (tttt) cc_final: 0.8947 (ptmm) REVERT: A 481 ASP cc_start: 0.8309 (p0) cc_final: 0.7660 (p0) REVERT: A 534 LEU cc_start: 0.8890 (tp) cc_final: 0.8649 (tp) REVERT: A 746 MET cc_start: 0.9383 (mtm) cc_final: 0.9027 (ttp) REVERT: A 1209 MET cc_start: 0.8723 (mmm) cc_final: 0.8469 (mmm) REVERT: A 1368 MET cc_start: 0.8760 (mtm) cc_final: 0.8304 (mtp) REVERT: A 1407 GLU cc_start: 0.9068 (tp30) cc_final: 0.8562 (tm-30) REVERT: B 314 LEU cc_start: 0.9377 (mt) cc_final: 0.9097 (mt) REVERT: B 489 SER cc_start: 0.9463 (t) cc_final: 0.9183 (p) REVERT: B 842 ASN cc_start: 0.9547 (t0) cc_final: 0.9277 (t0) REVERT: B 911 ILE cc_start: 0.9075 (mt) cc_final: 0.8848 (tp) REVERT: B 1136 ASP cc_start: 0.8820 (m-30) cc_final: 0.8505 (m-30) REVERT: B 1202 LEU cc_start: 0.9325 (mt) cc_final: 0.8976 (tt) REVERT: D 71 LYS cc_start: 0.6156 (mttt) cc_final: 0.5867 (mmtt) REVERT: D 159 THR cc_start: 0.7522 (m) cc_final: 0.7019 (p) REVERT: E 112 TYR cc_start: 0.9320 (p90) cc_final: 0.8192 (p90) REVERT: F 77 ASP cc_start: 0.8905 (p0) cc_final: 0.8469 (p0) REVERT: G 49 LEU cc_start: 0.8946 (mt) cc_final: 0.8652 (tp) REVERT: G 61 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8951 (tp) REVERT: G 88 ASP cc_start: 0.7320 (m-30) cc_final: 0.7012 (m-30) REVERT: G 150 CYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6394 (m) REVERT: H 21 ASN cc_start: 0.8662 (m-40) cc_final: 0.8267 (p0) REVERT: H 40 LEU cc_start: 0.8854 (tp) cc_final: 0.8283 (tt) REVERT: H 78 SER cc_start: 0.8519 (t) cc_final: 0.8265 (p) REVERT: I 47 GLU cc_start: 0.8143 (tt0) cc_final: 0.7742 (tt0) REVERT: I 84 VAL cc_start: 0.8178 (t) cc_final: 0.7765 (m) REVERT: I 86 PHE cc_start: 0.8271 (p90) cc_final: 0.7878 (p90) REVERT: J 14 VAL cc_start: 0.8530 (t) cc_final: 0.8282 (t) REVERT: L 33 GLU cc_start: 0.8646 (pt0) cc_final: 0.8382 (tm-30) REVERT: O 93 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8238 (mm-30) REVERT: O 104 MET cc_start: 0.9291 (ttm) cc_final: 0.8825 (tpt) REVERT: O 240 MET cc_start: 0.5029 (OUTLIER) cc_final: 0.3343 (mmt) REVERT: Q 365 TYR cc_start: 0.6665 (t80) cc_final: 0.6336 (t80) REVERT: U 20 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6869 (mt-10) REVERT: U 26 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8496 (tp30) REVERT: V 33 GLU cc_start: 0.2462 (OUTLIER) cc_final: 0.2161 (pm20) REVERT: V 78 PHE cc_start: 0.8568 (m-80) cc_final: 0.8200 (m-80) outliers start: 32 outliers final: 5 residues processed: 1090 average time/residue: 0.2701 time to fit residues: 470.5653 Evaluate side-chains 537 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 528 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 497 optimal weight: 40.0000 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 0.7980 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 516 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A 786 HIS ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 115 GLN B 178 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN B 516 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 HIS C 73 GLN C 79 GLN C 203 GLN D 37 GLN D 143 ASN D 173 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 GLN M 197 HIS O 88 HIS O 91 ASN Q 117 HIS R 223 GLN U 280 GLN V 55 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.056396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.042309 restraints weight = 316028.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.043562 restraints weight = 187301.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.044428 restraints weight = 129171.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044987 restraints weight = 98598.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.045455 restraints weight = 81409.783| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 42618 Z= 0.217 Angle : 0.827 26.476 57836 Z= 0.426 Chirality : 0.049 0.396 6559 Planarity : 0.006 0.093 7176 Dihedral : 14.438 101.536 6560 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 0.24 % Allowed : 3.11 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.11), residues: 5066 helix: -0.14 (0.11), residues: 1917 sheet: -0.91 (0.16), residues: 897 loop : -1.10 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A 344 TYR 0.029 0.002 TYR Q 373 PHE 0.038 0.002 PHE K 67 TRP 0.030 0.002 TRP U 42 HIS 0.017 0.002 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (42582) covalent geometry : angle 0.79260 / 0.42 (57791) hydrogen bonds : bond 0.05549 / 3.78 ( 1919) hydrogen bonds : angle 6.20802 / 4.39 ( 5437) metal coordination : bond 0.01657 / 0.85 ( 35) metal coordination : angle 8.44543 / 5.60 ( 45) Misc. bond : bond 0.01908 / 1.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 671 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.8380 (m-80) cc_final: 0.7634 (m-80) REVERT: A 76 GLU cc_start: 0.9222 (tp30) cc_final: 0.8851 (tm-30) REVERT: A 268 ASP cc_start: 0.9375 (m-30) cc_final: 0.9074 (m-30) REVERT: A 290 GLU cc_start: 0.9506 (pt0) cc_final: 0.9021 (mm-30) REVERT: A 307 ASP cc_start: 0.9572 (m-30) cc_final: 0.9172 (m-30) REVERT: A 323 LYS cc_start: 0.9202 (tptt) cc_final: 0.8886 (tptt) REVERT: A 326 ARG cc_start: 0.9274 (ttt-90) cc_final: 0.8559 (ttp80) REVERT: A 330 LYS cc_start: 0.9029 (tttt) cc_final: 0.8523 (ptmm) REVERT: A 340 LEU cc_start: 0.9750 (mt) cc_final: 0.9506 (mt) REVERT: A 431 LYS cc_start: 0.9454 (mppt) cc_final: 0.9014 (mmtm) REVERT: A 455 MET cc_start: 0.8083 (mtp) cc_final: 0.7769 (mtm) REVERT: A 487 MET cc_start: 0.8708 (mtp) cc_final: 0.7980 (mtp) REVERT: A 521 MET cc_start: 0.9213 (mmt) cc_final: 0.8806 (mmm) REVERT: A 748 MET cc_start: 0.9223 (ttp) cc_final: 0.8834 (ptm) REVERT: A 761 MET cc_start: 0.8974 (mpp) cc_final: 0.8527 (mpp) REVERT: A 838 GLN cc_start: 0.9336 (tm-30) cc_final: 0.9080 (tm-30) REVERT: A 854 ASN cc_start: 0.9579 (m-40) cc_final: 0.9282 (m-40) REVERT: A 873 MET cc_start: 0.9310 (mmp) cc_final: 0.8818 (mmm) REVERT: A 1209 MET cc_start: 0.9061 (mmm) cc_final: 0.8354 (mmm) REVERT: A 1285 MET cc_start: 0.9240 (tpt) cc_final: 0.8930 (tpp) REVERT: A 1317 MET cc_start: 0.8636 (tmm) cc_final: 0.8312 (tpt) REVERT: A 1336 MET cc_start: 0.9664 (tpt) cc_final: 0.9348 (tpp) REVERT: A 1368 MET cc_start: 0.8959 (mtm) cc_final: 0.8752 (mtm) REVERT: A 1398 MET cc_start: 0.9567 (mmt) cc_final: 0.9189 (mmt) REVERT: B 122 LEU cc_start: 0.9455 (mt) cc_final: 0.9185 (mt) REVERT: B 173 MET cc_start: 0.8463 (ttm) cc_final: 0.7911 (tpp) REVERT: B 199 MET cc_start: 0.8017 (tpt) cc_final: 0.7812 (tpt) REVERT: B 371 GLU cc_start: 0.9271 (mp0) cc_final: 0.9057 (mp0) REVERT: B 412 LEU cc_start: 0.9477 (mt) cc_final: 0.9197 (mt) REVERT: B 417 PHE cc_start: 0.9400 (t80) cc_final: 0.8991 (t80) REVERT: B 466 TRP cc_start: 0.7623 (m-90) cc_final: 0.7373 (m-90) REVERT: B 542 MET cc_start: 0.8948 (mtp) cc_final: 0.8748 (mmm) REVERT: B 678 GLU cc_start: 0.8707 (tt0) cc_final: 0.8431 (mm-30) REVERT: B 696 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8810 (mm-30) REVERT: B 773 MET cc_start: 0.9329 (mtm) cc_final: 0.9024 (mtt) REVERT: B 837 ASP cc_start: 0.8679 (m-30) cc_final: 0.8418 (t0) REVERT: B 839 MET cc_start: 0.9235 (ptp) cc_final: 0.9016 (ptp) REVERT: B 846 ILE cc_start: 0.9679 (mt) cc_final: 0.9407 (mt) REVERT: B 861 ASP cc_start: 0.8400 (t0) cc_final: 0.8165 (t70) REVERT: B 908 GLU cc_start: 0.8680 (mp0) cc_final: 0.8357 (tm-30) REVERT: B 1072 MET cc_start: 0.8304 (mmm) cc_final: 0.8002 (mmm) REVERT: B 1082 MET cc_start: 0.8821 (tpt) cc_final: 0.8277 (tpp) REVERT: B 1120 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8569 (mm-30) REVERT: B 1136 ASP cc_start: 0.9049 (m-30) cc_final: 0.8497 (m-30) REVERT: B 1202 LEU cc_start: 0.9604 (mt) cc_final: 0.9024 (mt) REVERT: B 1203 LEU cc_start: 0.9376 (mm) cc_final: 0.8847 (mm) REVERT: B 1210 MET cc_start: 0.8933 (tpt) cc_final: 0.7872 (tpp) REVERT: C 16 ASP cc_start: 0.8692 (p0) cc_final: 0.8250 (p0) REVERT: C 72 LEU cc_start: 0.9405 (mt) cc_final: 0.9198 (mt) REVERT: C 259 LEU cc_start: 0.9657 (mt) cc_final: 0.9390 (mt) REVERT: D 173 HIS cc_start: 0.9095 (m90) cc_final: 0.8613 (m90) REVERT: E 112 TYR cc_start: 0.9382 (p90) cc_final: 0.8281 (p90) REVERT: E 182 ASP cc_start: 0.9164 (t0) cc_final: 0.8860 (t0) REVERT: F 87 LYS cc_start: 0.9267 (pttm) cc_final: 0.8986 (pttm) REVERT: F 94 LEU cc_start: 0.9771 (mm) cc_final: 0.9539 (mm) REVERT: G 22 MET cc_start: 0.9690 (ptp) cc_final: 0.9343 (ptm) REVERT: G 88 ASP cc_start: 0.7371 (m-30) cc_final: 0.6924 (m-30) REVERT: G 166 ASP cc_start: 0.8120 (t0) cc_final: 0.7803 (t0) REVERT: H 21 ASN cc_start: 0.9152 (m-40) cc_final: 0.8491 (p0) REVERT: H 22 LYS cc_start: 0.9448 (mttt) cc_final: 0.8916 (mtpp) REVERT: H 27 GLU cc_start: 0.8564 (mp0) cc_final: 0.8150 (mp0) REVERT: H 40 LEU cc_start: 0.9382 (tp) cc_final: 0.9094 (tt) REVERT: H 142 LEU cc_start: 0.9598 (tp) cc_final: 0.9186 (tp) REVERT: I 47 GLU cc_start: 0.8908 (tt0) cc_final: 0.8508 (tt0) REVERT: I 61 ASP cc_start: 0.7634 (m-30) cc_final: 0.7385 (m-30) REVERT: I 84 VAL cc_start: 0.9253 (t) cc_final: 0.8921 (m) REVERT: I 86 PHE cc_start: 0.9458 (p90) cc_final: 0.8462 (p90) REVERT: J 27 GLU cc_start: 0.9317 (mm-30) cc_final: 0.9032 (mm-30) REVERT: J 49 MET cc_start: 0.9339 (mmp) cc_final: 0.8556 (mmm) REVERT: K 1 MET cc_start: 0.7892 (ptp) cc_final: 0.7140 (ppp) REVERT: K 22 ASP cc_start: 0.9418 (m-30) cc_final: 0.8993 (m-30) REVERT: K 36 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8376 (tp30) REVERT: K 73 LEU cc_start: 0.9725 (tp) cc_final: 0.9452 (tt) REVERT: K 85 ASP cc_start: 0.9100 (m-30) cc_final: 0.8628 (t70) REVERT: L 40 LEU cc_start: 0.9550 (pp) cc_final: 0.9256 (pp) REVERT: M 242 PHE cc_start: 0.9623 (m-80) cc_final: 0.8952 (m-80) REVERT: O 93 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8053 (mm-30) REVERT: O 104 MET cc_start: 0.8983 (ttm) cc_final: 0.8593 (tpt) REVERT: Q 401 TYR cc_start: 0.8443 (p90) cc_final: 0.7910 (p90) REVERT: R 274 ASN cc_start: 0.9030 (t0) cc_final: 0.8817 (p0) REVERT: U 244 MET cc_start: 0.9302 (ttp) cc_final: 0.8934 (ttm) REVERT: U 262 LEU cc_start: 0.9106 (mt) cc_final: 0.8460 (mt) REVERT: V 54 ASP cc_start: 0.8129 (t70) cc_final: 0.7748 (m-30) outliers start: 10 outliers final: 2 residues processed: 680 average time/residue: 0.2391 time to fit residues: 268.9839 Evaluate side-chains 472 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 470 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 311 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 392 optimal weight: 4.9990 chunk 459 optimal weight: 7.9990 chunk 319 optimal weight: 0.4980 chunk 261 optimal weight: 4.9990 chunk 334 optimal weight: 6.9990 chunk 326 optimal weight: 3.9990 chunk 356 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 476 optimal weight: 20.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN A 736 ASN A 881 GLN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN A1354 ASN B 215 GLN B 516 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 137 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.054834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040955 restraints weight = 319096.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.042141 restraints weight = 191333.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042981 restraints weight = 133205.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.043516 restraints weight = 102648.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043962 restraints weight = 85086.431| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 42618 Z= 0.224 Angle : 0.752 25.342 57836 Z= 0.385 Chirality : 0.046 0.349 6559 Planarity : 0.005 0.092 7176 Dihedral : 14.378 104.739 6560 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.01 % Favored : 94.75 % Rotamer: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.11), residues: 5066 helix: 0.65 (0.11), residues: 1951 sheet: -0.80 (0.16), residues: 887 loop : -0.99 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 928 TYR 0.030 0.002 TYR G 44 PHE 0.033 0.002 PHE A 211 TRP 0.030 0.002 TRP U 42 HIS 0.016 0.002 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (42582) covalent geometry : angle 0.71580 / 0.38 (57791) hydrogen bonds : bond 0.04744 / 3.23 ( 1919) hydrogen bonds : angle 5.71894 / 4.04 ( 5437) metal coordination : bond 0.01578 / 0.81 ( 35) metal coordination : angle 8.31290 / 5.27 ( 45) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 584 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.9684 (tt0) cc_final: 0.9426 (tm-30) REVERT: A 30 ILE cc_start: 0.9494 (pt) cc_final: 0.9239 (pt) REVERT: A 76 GLU cc_start: 0.9362 (tp30) cc_final: 0.8995 (tm-30) REVERT: A 234 MET cc_start: 0.9600 (ttm) cc_final: 0.9143 (ttt) REVERT: A 268 ASP cc_start: 0.9086 (m-30) cc_final: 0.8783 (m-30) REVERT: A 290 GLU cc_start: 0.9655 (pt0) cc_final: 0.9157 (mm-30) REVERT: A 307 ASP cc_start: 0.9586 (m-30) cc_final: 0.9218 (t0) REVERT: A 326 ARG cc_start: 0.9186 (ttt-90) cc_final: 0.8684 (ttp80) REVERT: A 340 LEU cc_start: 0.9789 (mt) cc_final: 0.9545 (mt) REVERT: A 431 LYS cc_start: 0.9498 (mppt) cc_final: 0.9040 (mmtm) REVERT: A 487 MET cc_start: 0.9106 (mtp) cc_final: 0.8356 (mtp) REVERT: A 521 MET cc_start: 0.9290 (mmt) cc_final: 0.8947 (mmm) REVERT: A 546 VAL cc_start: 0.9458 (t) cc_final: 0.9119 (t) REVERT: A 549 MET cc_start: 0.9539 (mtt) cc_final: 0.8906 (mpp) REVERT: A 748 MET cc_start: 0.9300 (ttp) cc_final: 0.8910 (ptm) REVERT: A 761 MET cc_start: 0.8991 (mpp) cc_final: 0.8678 (mpp) REVERT: A 818 MET cc_start: 0.9254 (mtt) cc_final: 0.8875 (mmt) REVERT: A 838 GLN cc_start: 0.9345 (tm-30) cc_final: 0.9055 (tm-30) REVERT: A 854 ASN cc_start: 0.9614 (m-40) cc_final: 0.9361 (m-40) REVERT: A 873 MET cc_start: 0.9361 (mmp) cc_final: 0.8946 (mmm) REVERT: A 1105 LEU cc_start: 0.9580 (tp) cc_final: 0.9338 (tt) REVERT: A 1207 LEU cc_start: 0.9023 (mt) cc_final: 0.8792 (mp) REVERT: A 1209 MET cc_start: 0.9120 (mmm) cc_final: 0.8363 (mmm) REVERT: A 1265 ASN cc_start: 0.9318 (m110) cc_final: 0.9083 (m-40) REVERT: A 1267 MET cc_start: 0.9368 (mtm) cc_final: 0.9160 (mtm) REVERT: A 1285 MET cc_start: 0.9204 (tpt) cc_final: 0.8920 (tpp) REVERT: A 1317 MET cc_start: 0.8550 (tmm) cc_final: 0.8291 (tmm) REVERT: A 1336 MET cc_start: 0.9655 (tpt) cc_final: 0.9381 (tpt) REVERT: A 1368 MET cc_start: 0.8900 (mtm) cc_final: 0.8643 (mtm) REVERT: A 1376 THR cc_start: 0.9548 (m) cc_final: 0.8827 (m) REVERT: A 1398 MET cc_start: 0.9428 (mmt) cc_final: 0.9198 (mmt) REVERT: A 1448 GLU cc_start: 0.9610 (mp0) cc_final: 0.9319 (mp0) REVERT: B 92 PHE cc_start: 0.9499 (m-80) cc_final: 0.9069 (m-80) REVERT: B 173 MET cc_start: 0.8569 (ttm) cc_final: 0.7730 (tpp) REVERT: B 199 MET cc_start: 0.8107 (tpt) cc_final: 0.7394 (tpt) REVERT: B 371 GLU cc_start: 0.9248 (mp0) cc_final: 0.8877 (mp0) REVERT: B 417 PHE cc_start: 0.9364 (t80) cc_final: 0.8874 (t80) REVERT: B 438 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8903 (mt-10) REVERT: B 696 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8883 (mm-30) REVERT: B 705 MET cc_start: 0.8484 (mmt) cc_final: 0.7999 (mmm) REVERT: B 773 MET cc_start: 0.9401 (mtm) cc_final: 0.8880 (mtt) REVERT: B 837 ASP cc_start: 0.8901 (m-30) cc_final: 0.8398 (t0) REVERT: B 839 MET cc_start: 0.9256 (ptp) cc_final: 0.8605 (mpp) REVERT: B 841 MET cc_start: 0.8953 (ttm) cc_final: 0.8624 (tpp) REVERT: B 861 ASP cc_start: 0.8404 (t0) cc_final: 0.8121 (t70) REVERT: B 1072 MET cc_start: 0.8237 (mmm) cc_final: 0.7899 (mmm) REVERT: B 1082 MET cc_start: 0.8561 (tpt) cc_final: 0.8147 (tpp) REVERT: B 1132 GLU cc_start: 0.8799 (pp20) cc_final: 0.8473 (tm-30) REVERT: B 1133 MET cc_start: 0.9257 (mtp) cc_final: 0.8674 (mtp) REVERT: B 1136 ASP cc_start: 0.9484 (m-30) cc_final: 0.8333 (m-30) REVERT: B 1138 MET cc_start: 0.9568 (mmm) cc_final: 0.9116 (mmm) REVERT: B 1152 MET cc_start: 0.8593 (tpt) cc_final: 0.8253 (tpt) REVERT: B 1203 LEU cc_start: 0.9301 (mm) cc_final: 0.9007 (mm) REVERT: B 1204 PHE cc_start: 0.9702 (m-10) cc_final: 0.9396 (m-80) REVERT: B 1208 MET cc_start: 0.9454 (mtp) cc_final: 0.9172 (mtt) REVERT: B 1210 MET cc_start: 0.9199 (tpt) cc_final: 0.8697 (tpp) REVERT: C 259 LEU cc_start: 0.9686 (mt) cc_final: 0.9354 (mt) REVERT: E 22 MET cc_start: 0.9371 (ppp) cc_final: 0.9165 (ppp) REVERT: E 112 TYR cc_start: 0.9370 (p90) cc_final: 0.8221 (p90) REVERT: E 182 ASP cc_start: 0.9175 (t0) cc_final: 0.8773 (t0) REVERT: E 211 TYR cc_start: 0.8883 (m-80) cc_final: 0.8680 (m-10) REVERT: F 85 MET cc_start: 0.8505 (tmm) cc_final: 0.8100 (tmm) REVERT: F 87 LYS cc_start: 0.9275 (pttm) cc_final: 0.9017 (pttm) REVERT: F 112 GLU cc_start: 0.8967 (pm20) cc_final: 0.8640 (pm20) REVERT: F 114 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8076 (mm-30) REVERT: F 124 GLU cc_start: 0.9001 (tt0) cc_final: 0.8751 (tt0) REVERT: F 136 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7782 (mtt180) REVERT: G 22 MET cc_start: 0.9635 (ptp) cc_final: 0.9254 (ptm) REVERT: G 44 TYR cc_start: 0.8454 (m-10) cc_final: 0.8228 (m-10) REVERT: G 88 ASP cc_start: 0.7361 (m-30) cc_final: 0.6991 (m-30) REVERT: G 106 MET cc_start: 0.6808 (mtt) cc_final: 0.6598 (mtt) REVERT: G 166 ASP cc_start: 0.8004 (t0) cc_final: 0.7618 (t0) REVERT: H 21 ASN cc_start: 0.9248 (m-40) cc_final: 0.8476 (p0) REVERT: H 22 LYS cc_start: 0.9449 (mttt) cc_final: 0.8947 (mtpp) REVERT: H 27 GLU cc_start: 0.8613 (mp0) cc_final: 0.8361 (mp0) REVERT: H 40 LEU cc_start: 0.9469 (tp) cc_final: 0.9199 (tt) REVERT: H 97 MET cc_start: 0.8975 (mtp) cc_final: 0.8732 (mtp) REVERT: H 142 LEU cc_start: 0.9654 (tp) cc_final: 0.9180 (tp) REVERT: I 47 GLU cc_start: 0.8959 (tt0) cc_final: 0.8596 (tt0) REVERT: I 61 ASP cc_start: 0.7723 (m-30) cc_final: 0.7517 (m-30) REVERT: I 86 PHE cc_start: 0.9461 (p90) cc_final: 0.9201 (p90) REVERT: I 94 ASP cc_start: 0.9148 (m-30) cc_final: 0.8500 (p0) REVERT: J 27 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9108 (mm-30) REVERT: J 38 ARG cc_start: 0.9133 (ttm110) cc_final: 0.8912 (ttm110) REVERT: J 49 MET cc_start: 0.9304 (mmp) cc_final: 0.8593 (mmm) REVERT: K 1 MET cc_start: 0.7883 (ptp) cc_final: 0.7243 (ppp) REVERT: K 22 ASP cc_start: 0.9413 (m-30) cc_final: 0.8984 (m-30) REVERT: K 36 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8607 (tp30) REVERT: K 85 ASP cc_start: 0.9135 (m-30) cc_final: 0.8682 (t70) REVERT: L 40 LEU cc_start: 0.9557 (pp) cc_final: 0.9331 (pp) REVERT: M 55 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8222 (mtmt) REVERT: Q 336 ASP cc_start: 0.6484 (t70) cc_final: 0.6266 (t70) REVERT: Q 365 TYR cc_start: 0.8902 (t80) cc_final: 0.8507 (t80) REVERT: U 244 MET cc_start: 0.9230 (ttp) cc_final: 0.9003 (ttm) REVERT: U 262 LEU cc_start: 0.8626 (mt) cc_final: 0.8354 (mt) REVERT: V 54 ASP cc_start: 0.8176 (t70) cc_final: 0.7849 (m-30) REVERT: V 78 PHE cc_start: 0.8741 (m-80) cc_final: 0.8162 (m-80) outliers start: 5 outliers final: 0 residues processed: 587 average time/residue: 0.2368 time to fit residues: 229.9537 Evaluate side-chains 438 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 223 optimal weight: 0.7980 chunk 352 optimal weight: 9.9990 chunk 370 optimal weight: 2.9990 chunk 287 optimal weight: 20.0000 chunk 463 optimal weight: 50.0000 chunk 354 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 497 optimal weight: 40.0000 chunk 282 optimal weight: 20.0000 chunk 507 optimal weight: 30.0000 chunk 321 optimal weight: 10.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 299 HIS ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN D 173 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN M 197 HIS Q 99 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.052893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.039221 restraints weight = 329442.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.040387 restraints weight = 196923.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.041201 restraints weight = 137042.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041730 restraints weight = 104831.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.042162 restraints weight = 86812.899| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 42618 Z= 0.291 Angle : 0.796 26.907 57836 Z= 0.406 Chirality : 0.046 0.451 6559 Planarity : 0.006 0.101 7176 Dihedral : 14.505 104.508 6560 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.65 % Favored : 94.12 % Rotamer: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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 are not related in a simple way. whole: -0.51 (0.11), residues: 5066 helix: 0.64 (0.11), residues: 1977 sheet: -0.77 (0.17), residues: 890 loop : -0.97 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 80 TYR 0.021 0.002 TYR G 25 PHE 0.049 0.002 PHE K 67 TRP 0.021 0.002 TRP U 42 HIS 0.020 0.002 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.29 (42582) covalent geometry : angle 0.75693 / 0.40 (57791) hydrogen bonds : bond 0.04897 / 3.32 ( 1919) hydrogen bonds : angle 5.68502 / 3.99 ( 5437) metal coordination : bond 0.01909 / 1.07 ( 35) metal coordination : angle 8.82875 / 5.72 ( 45) Misc. bond : bond 0.00146 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 506 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8642 (mp0) cc_final: 0.7844 (mp0) REVERT: A 76 GLU cc_start: 0.9452 (tp30) cc_final: 0.9128 (tm-30) REVERT: A 234 MET cc_start: 0.9522 (ttm) cc_final: 0.9302 (ttt) REVERT: A 268 ASP cc_start: 0.9172 (m-30) cc_final: 0.8895 (m-30) REVERT: A 307 ASP cc_start: 0.9626 (m-30) cc_final: 0.9325 (t0) REVERT: A 326 ARG cc_start: 0.9210 (ttt-90) cc_final: 0.8685 (ttp80) REVERT: A 340 LEU cc_start: 0.9791 (mt) cc_final: 0.9540 (mt) REVERT: A 353 ILE cc_start: 0.9771 (pt) cc_final: 0.9554 (mp) REVERT: A 455 MET cc_start: 0.8845 (mtm) cc_final: 0.8265 (mtm) REVERT: A 456 MET cc_start: 0.9123 (mmp) cc_final: 0.8204 (mmm) REVERT: A 482 PHE cc_start: 0.8682 (m-80) cc_final: 0.8307 (m-80) REVERT: A 487 MET cc_start: 0.8998 (mtp) cc_final: 0.8142 (mtp) REVERT: A 521 MET cc_start: 0.9312 (mmt) cc_final: 0.9051 (mmm) REVERT: A 748 MET cc_start: 0.9384 (ttp) cc_final: 0.8958 (ptm) REVERT: A 818 MET cc_start: 0.9424 (mtt) cc_final: 0.8916 (mmt) REVERT: A 854 ASN cc_start: 0.9623 (m-40) cc_final: 0.9383 (m-40) REVERT: A 873 MET cc_start: 0.9382 (mmp) cc_final: 0.8674 (mmm) REVERT: A 1209 MET cc_start: 0.9089 (mmm) cc_final: 0.8475 (mmm) REVERT: A 1265 ASN cc_start: 0.9331 (m110) cc_final: 0.9100 (m-40) REVERT: A 1285 MET cc_start: 0.9309 (tpt) cc_final: 0.8961 (tpp) REVERT: A 1317 MET cc_start: 0.8524 (tmm) cc_final: 0.7918 (tmm) REVERT: A 1336 MET cc_start: 0.9667 (tpt) cc_final: 0.9461 (tpp) REVERT: A 1368 MET cc_start: 0.8837 (mtm) cc_final: 0.8573 (mtm) REVERT: A 1448 GLU cc_start: 0.9593 (mp0) cc_final: 0.9309 (mp0) REVERT: B 92 PHE cc_start: 0.9527 (m-80) cc_final: 0.9117 (m-80) REVERT: B 199 MET cc_start: 0.8211 (tpt) cc_final: 0.7398 (tpp) REVERT: B 400 HIS cc_start: 0.9435 (t-90) cc_final: 0.9197 (t-90) REVERT: B 417 PHE cc_start: 0.9345 (t80) cc_final: 0.8893 (t80) REVERT: B 421 PHE cc_start: 0.9309 (t80) cc_final: 0.9080 (t80) REVERT: B 432 MET cc_start: 0.9343 (ptp) cc_final: 0.9089 (ptp) REVERT: B 438 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8900 (mt-10) REVERT: B 637 LEU cc_start: 0.9184 (tp) cc_final: 0.8786 (tp) REVERT: B 696 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8741 (mm-30) REVERT: B 773 MET cc_start: 0.9234 (mtm) cc_final: 0.8804 (mtt) REVERT: B 789 MET cc_start: 0.9162 (mmm) cc_final: 0.8821 (mmm) REVERT: B 837 ASP cc_start: 0.8938 (m-30) cc_final: 0.8721 (t0) REVERT: B 839 MET cc_start: 0.9291 (ptp) cc_final: 0.8781 (mpp) REVERT: B 841 MET cc_start: 0.9079 (ttm) cc_final: 0.8827 (tpp) REVERT: B 861 ASP cc_start: 0.8545 (t0) cc_final: 0.8266 (t70) REVERT: B 1082 MET cc_start: 0.8497 (tpt) cc_final: 0.8214 (tpp) REVERT: B 1111 MET cc_start: 0.9028 (mmm) cc_final: 0.8338 (mmp) REVERT: B 1132 GLU cc_start: 0.8900 (pp20) cc_final: 0.8420 (tm-30) REVERT: B 1133 MET cc_start: 0.9360 (mtp) cc_final: 0.9067 (mtp) REVERT: B 1136 ASP cc_start: 0.9440 (m-30) cc_final: 0.8769 (m-30) REVERT: B 1138 MET cc_start: 0.9511 (mmm) cc_final: 0.9057 (mmm) REVERT: B 1208 MET cc_start: 0.9504 (mtp) cc_final: 0.9041 (mtm) REVERT: B 1210 MET cc_start: 0.9348 (tpt) cc_final: 0.9039 (tpp) REVERT: C 72 LEU cc_start: 0.9382 (mt) cc_final: 0.9102 (mt) REVERT: C 259 LEU cc_start: 0.9669 (mt) cc_final: 0.9322 (mt) REVERT: E 22 MET cc_start: 0.9396 (ppp) cc_final: 0.9171 (ppp) REVERT: E 82 PHE cc_start: 0.8625 (m-80) cc_final: 0.8134 (m-80) REVERT: E 182 ASP cc_start: 0.9182 (t0) cc_final: 0.8807 (t0) REVERT: F 84 TYR cc_start: 0.9087 (m-80) cc_final: 0.8828 (m-80) REVERT: F 97 ARG cc_start: 0.9659 (tpm170) cc_final: 0.9189 (tpp-160) REVERT: G 21 ARG cc_start: 0.8925 (pmt-80) cc_final: 0.8560 (pmt-80) REVERT: G 22 MET cc_start: 0.9646 (ptp) cc_final: 0.9243 (ptm) REVERT: G 25 TYR cc_start: 0.9550 (m-80) cc_final: 0.9230 (m-80) REVERT: G 44 TYR cc_start: 0.8607 (m-10) cc_final: 0.8391 (m-10) REVERT: G 88 ASP cc_start: 0.7128 (m-30) cc_final: 0.6615 (m-30) REVERT: G 115 MET cc_start: 0.4608 (mmm) cc_final: 0.4259 (mmm) REVERT: G 166 ASP cc_start: 0.7928 (t0) cc_final: 0.7488 (t0) REVERT: H 21 ASN cc_start: 0.9249 (m-40) cc_final: 0.8329 (p0) REVERT: H 22 LYS cc_start: 0.9444 (mttt) cc_final: 0.8950 (mtpp) REVERT: H 40 LEU cc_start: 0.9472 (tp) cc_final: 0.9227 (tt) REVERT: H 97 MET cc_start: 0.9024 (mtp) cc_final: 0.8757 (mtp) REVERT: H 142 LEU cc_start: 0.9634 (tp) cc_final: 0.9145 (tp) REVERT: I 47 GLU cc_start: 0.9175 (tt0) cc_final: 0.8843 (tt0) REVERT: I 86 PHE cc_start: 0.9455 (p90) cc_final: 0.9179 (p90) REVERT: J 49 MET cc_start: 0.9309 (mmp) cc_final: 0.8601 (mmm) REVERT: K 22 ASP cc_start: 0.9428 (m-30) cc_final: 0.8995 (m-30) REVERT: K 54 ARG cc_start: 0.8845 (ppt170) cc_final: 0.8549 (ppt90) REVERT: K 85 ASP cc_start: 0.9170 (m-30) cc_final: 0.8702 (t70) REVERT: L 29 TYR cc_start: 0.9022 (m-80) cc_final: 0.8275 (m-80) REVERT: L 40 LEU cc_start: 0.9656 (pp) cc_final: 0.9342 (pp) REVERT: M 55 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8452 (mtmm) REVERT: Q 336 ASP cc_start: 0.6422 (t70) cc_final: 0.5744 (t0) REVERT: Q 375 LEU cc_start: 0.8813 (tp) cc_final: 0.8581 (tp) REVERT: R 263 MET cc_start: 0.9437 (mmm) cc_final: 0.9229 (mmm) REVERT: R 274 ASN cc_start: 0.9179 (t0) cc_final: 0.8908 (p0) REVERT: U 244 MET cc_start: 0.9302 (ttp) cc_final: 0.9098 (ttm) REVERT: V 54 ASP cc_start: 0.8205 (t70) cc_final: 0.7886 (m-30) outliers start: 2 outliers final: 1 residues processed: 507 average time/residue: 0.2358 time to fit residues: 200.7243 Evaluate side-chains 390 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 99 optimal weight: 1.9990 chunk 448 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 278 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 506 optimal weight: 50.0000 chunk 455 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 316 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN B1193 GLN D 51 ASN D 173 HIS E 32 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039833 restraints weight = 320973.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.040983 restraints weight = 192215.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.041822 restraints weight = 133817.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.042381 restraints weight = 102735.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.042753 restraints weight = 84944.421| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 42618 Z= 0.167 Angle : 0.686 25.899 57836 Z= 0.348 Chirality : 0.044 0.251 6559 Planarity : 0.005 0.081 7176 Dihedral : 14.372 103.629 6560 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.21 % Favored : 94.53 % Rotamer: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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 are not related in a simple way. whole: -0.19 (0.12), residues: 5066 helix: 0.98 (0.12), residues: 1980 sheet: -0.59 (0.17), residues: 851 loop : -0.87 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1055 TYR 0.036 0.002 TYR Q 373 PHE 0.023 0.002 PHE M 130 TRP 0.015 0.002 TRP B 586 HIS 0.010 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (42582) covalent geometry : angle 0.64569 / 0.35 (57791) hydrogen bonds : bond 0.04080 / 2.76 ( 1919) hydrogen bonds : angle 5.37818 / 3.78 ( 5437) metal coordination : bond 0.01335 / 0.69 ( 35) metal coordination : angle 8.35692 / 5.31 ( 45) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 530 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8734 (mp0) cc_final: 0.7989 (mp0) REVERT: A 76 GLU cc_start: 0.9367 (tp30) cc_final: 0.9079 (tm-30) REVERT: A 122 MET cc_start: 0.8796 (mtp) cc_final: 0.8540 (mtp) REVERT: A 268 ASP cc_start: 0.9205 (m-30) cc_final: 0.8931 (m-30) REVERT: A 304 MET cc_start: 0.8897 (mtp) cc_final: 0.8556 (mtm) REVERT: A 307 ASP cc_start: 0.9582 (m-30) cc_final: 0.9275 (t0) REVERT: A 326 ARG cc_start: 0.9175 (ttt-90) cc_final: 0.8673 (ttp80) REVERT: A 340 LEU cc_start: 0.9801 (mt) cc_final: 0.9457 (mt) REVERT: A 341 MET cc_start: 0.8567 (mmt) cc_final: 0.7862 (mmt) REVERT: A 431 LYS cc_start: 0.9515 (mppt) cc_final: 0.9117 (mmtm) REVERT: A 453 MET cc_start: 0.9683 (pmm) cc_final: 0.9365 (pmm) REVERT: A 455 MET cc_start: 0.8754 (mtm) cc_final: 0.8443 (mtm) REVERT: A 456 MET cc_start: 0.9180 (mmp) cc_final: 0.8256 (mmm) REVERT: A 487 MET cc_start: 0.8844 (mtp) cc_final: 0.7978 (mtp) REVERT: A 521 MET cc_start: 0.9319 (mmt) cc_final: 0.9083 (mmm) REVERT: A 545 GLN cc_start: 0.8977 (tp40) cc_final: 0.8531 (tp-100) REVERT: A 676 MET cc_start: 0.9022 (mtm) cc_final: 0.8786 (ptt) REVERT: A 748 MET cc_start: 0.9364 (ttp) cc_final: 0.9015 (ptm) REVERT: A 818 MET cc_start: 0.9364 (mtt) cc_final: 0.9154 (mmt) REVERT: A 873 MET cc_start: 0.9321 (mmp) cc_final: 0.8825 (mmm) REVERT: A 1062 GLU cc_start: 0.8961 (tp30) cc_final: 0.8734 (tp30) REVERT: A 1209 MET cc_start: 0.8978 (mmm) cc_final: 0.8162 (mmm) REVERT: A 1265 ASN cc_start: 0.9322 (m110) cc_final: 0.9116 (m-40) REVERT: A 1285 MET cc_start: 0.9300 (tpt) cc_final: 0.8953 (tpp) REVERT: A 1317 MET cc_start: 0.8493 (tmm) cc_final: 0.7846 (tmm) REVERT: A 1368 MET cc_start: 0.8796 (mtm) cc_final: 0.8570 (mtm) REVERT: A 1376 THR cc_start: 0.9529 (m) cc_final: 0.9264 (t) REVERT: A 1409 LEU cc_start: 0.9674 (mt) cc_final: 0.9456 (pp) REVERT: A 1433 MET cc_start: 0.9061 (tpt) cc_final: 0.8656 (tpp) REVERT: B 92 PHE cc_start: 0.9400 (m-80) cc_final: 0.9127 (m-80) REVERT: B 199 MET cc_start: 0.8072 (tpt) cc_final: 0.7273 (tpp) REVERT: B 417 PHE cc_start: 0.9290 (t80) cc_final: 0.8890 (t80) REVERT: B 421 PHE cc_start: 0.9301 (t80) cc_final: 0.9101 (t80) REVERT: B 432 MET cc_start: 0.9330 (ptp) cc_final: 0.9012 (ptp) REVERT: B 542 MET cc_start: 0.9129 (mmm) cc_final: 0.8573 (tpp) REVERT: B 552 MET cc_start: 0.9486 (tpp) cc_final: 0.9093 (tpp) REVERT: B 637 LEU cc_start: 0.9147 (tp) cc_final: 0.8733 (tp) REVERT: B 705 MET cc_start: 0.8377 (mmt) cc_final: 0.8139 (mmm) REVERT: B 773 MET cc_start: 0.9167 (mtm) cc_final: 0.8833 (mtt) REVERT: B 789 MET cc_start: 0.9157 (mmm) cc_final: 0.8868 (mmm) REVERT: B 839 MET cc_start: 0.9255 (ptp) cc_final: 0.8795 (mpp) REVERT: B 841 MET cc_start: 0.9047 (ttm) cc_final: 0.8795 (tpp) REVERT: B 1082 MET cc_start: 0.8496 (tpt) cc_final: 0.8134 (tpp) REVERT: B 1111 MET cc_start: 0.9004 (mmm) cc_final: 0.8567 (mmm) REVERT: B 1132 GLU cc_start: 0.8880 (pp20) cc_final: 0.8354 (pp20) REVERT: B 1133 MET cc_start: 0.9342 (mtp) cc_final: 0.8989 (mtp) REVERT: B 1136 ASP cc_start: 0.9406 (m-30) cc_final: 0.8640 (m-30) REVERT: B 1138 MET cc_start: 0.9537 (mmm) cc_final: 0.9122 (mmm) REVERT: B 1208 MET cc_start: 0.9405 (mtp) cc_final: 0.8992 (mtm) REVERT: B 1210 MET cc_start: 0.9259 (tpt) cc_final: 0.9036 (tpp) REVERT: C 33 LEU cc_start: 0.9676 (mm) cc_final: 0.9331 (mm) REVERT: C 72 LEU cc_start: 0.9333 (mt) cc_final: 0.9034 (tp) REVERT: E 22 MET cc_start: 0.9333 (ppp) cc_final: 0.9098 (ppp) REVERT: E 58 MET cc_start: 0.8394 (mtm) cc_final: 0.8189 (mtt) REVERT: E 82 PHE cc_start: 0.8529 (m-80) cc_final: 0.7996 (m-80) REVERT: E 93 MET cc_start: 0.9323 (tmm) cc_final: 0.9064 (tmm) REVERT: E 112 TYR cc_start: 0.9354 (p90) cc_final: 0.8223 (p90) REVERT: E 182 ASP cc_start: 0.9147 (t0) cc_final: 0.8765 (t70) REVERT: E 215 MET cc_start: 0.7981 (mmp) cc_final: 0.7733 (mmm) REVERT: F 85 MET cc_start: 0.8558 (tmm) cc_final: 0.8337 (tmm) REVERT: F 100 GLN cc_start: 0.9584 (mp10) cc_final: 0.9094 (mm-40) REVERT: F 124 GLU cc_start: 0.9145 (tt0) cc_final: 0.8911 (tt0) REVERT: G 22 MET cc_start: 0.9575 (ptp) cc_final: 0.9222 (ptm) REVERT: G 25 TYR cc_start: 0.9528 (m-80) cc_final: 0.9115 (m-80) REVERT: G 44 TYR cc_start: 0.8605 (m-10) cc_final: 0.8359 (m-10) REVERT: G 88 ASP cc_start: 0.7329 (m-30) cc_final: 0.6936 (m-30) REVERT: G 115 MET cc_start: 0.4843 (mmm) cc_final: 0.4491 (mmm) REVERT: G 166 ASP cc_start: 0.7944 (t0) cc_final: 0.7516 (t0) REVERT: H 21 ASN cc_start: 0.9184 (m-40) cc_final: 0.8274 (p0) REVERT: H 22 LYS cc_start: 0.9387 (mttt) cc_final: 0.8929 (mtpp) REVERT: H 40 LEU cc_start: 0.9509 (tp) cc_final: 0.9276 (tt) REVERT: H 97 MET cc_start: 0.8945 (mtp) cc_final: 0.8681 (mtp) REVERT: H 142 LEU cc_start: 0.9651 (tp) cc_final: 0.9083 (tp) REVERT: I 6 PHE cc_start: 0.7514 (m-10) cc_final: 0.7239 (m-80) REVERT: I 47 GLU cc_start: 0.9189 (tt0) cc_final: 0.8881 (tt0) REVERT: I 86 PHE cc_start: 0.9436 (p90) cc_final: 0.9158 (p90) REVERT: J 49 MET cc_start: 0.9262 (mmp) cc_final: 0.8547 (mmm) REVERT: K 22 ASP cc_start: 0.9352 (m-30) cc_final: 0.8484 (p0) REVERT: K 36 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8660 (mm-30) REVERT: K 50 LEU cc_start: 0.9585 (mt) cc_final: 0.9372 (mt) REVERT: K 67 PHE cc_start: 0.8949 (m-80) cc_final: 0.8738 (m-80) REVERT: K 85 ASP cc_start: 0.9126 (m-30) cc_final: 0.8705 (t70) REVERT: L 29 TYR cc_start: 0.8913 (m-80) cc_final: 0.8216 (m-80) REVERT: L 40 LEU cc_start: 0.9643 (pp) cc_final: 0.9315 (pp) REVERT: M 152 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8087 (mt-10) REVERT: M 158 HIS cc_start: 0.8082 (t70) cc_final: 0.7574 (t70) REVERT: Q 336 ASP cc_start: 0.6340 (t70) cc_final: 0.5957 (t0) REVERT: Q 344 PHE cc_start: 0.9238 (t80) cc_final: 0.9025 (t80) REVERT: Q 386 MET cc_start: 0.6900 (ppp) cc_final: 0.5869 (mmm) REVERT: R 274 ASN cc_start: 0.9194 (t0) cc_final: 0.8931 (p0) REVERT: U 244 MET cc_start: 0.9269 (ttp) cc_final: 0.9047 (ttm) outliers start: 1 outliers final: 0 residues processed: 530 average time/residue: 0.2280 time to fit residues: 203.6707 Evaluate side-chains 408 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 456 optimal weight: 6.9990 chunk 441 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 475 optimal weight: 30.0000 chunk 380 optimal weight: 6.9990 chunk 443 optimal weight: 5.9990 chunk 408 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 341 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN A 256 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A1009 ASN A1059 HIS ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 HIS C 79 GLN C 131 HIS D 51 ASN D 173 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.051938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038478 restraints weight = 336963.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.039628 restraints weight = 200807.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.040336 restraints weight = 139276.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.040920 restraints weight = 108288.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.041227 restraints weight = 89076.212| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 42618 Z= 0.270 Angle : 0.750 26.077 57836 Z= 0.383 Chirality : 0.044 0.303 6559 Planarity : 0.005 0.073 7176 Dihedral : 14.414 102.127 6560 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.16 % Favored : 93.58 % Rotamer: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.12), residues: 5066 helix: 0.87 (0.12), residues: 1975 sheet: -0.70 (0.17), residues: 882 loop : -0.90 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1055 TYR 0.022 0.002 TYR Q 373 PHE 0.028 0.002 PHE D 70 TRP 0.047 0.003 TRP R 81 HIS 0.009 0.002 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.27 (42582) covalent geometry : angle 0.71131 / 0.38 (57791) hydrogen bonds : bond 0.04533 / 3.06 ( 1919) hydrogen bonds : angle 5.47971 / 3.85 ( 5437) metal coordination : bond 0.01758 / 0.99 ( 35) metal coordination : angle 8.58438 / 5.54 ( 45) Misc. bond : bond 0.00075 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 467 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8930 (mp0) cc_final: 0.8222 (mp0) REVERT: A 76 GLU cc_start: 0.9410 (tp30) cc_final: 0.9169 (tm-30) REVERT: A 122 MET cc_start: 0.8924 (mtp) cc_final: 0.8687 (mtp) REVERT: A 340 LEU cc_start: 0.9814 (mt) cc_final: 0.9504 (mt) REVERT: A 341 MET cc_start: 0.8653 (mmt) cc_final: 0.8205 (mmm) REVERT: A 455 MET cc_start: 0.8783 (mtm) cc_final: 0.8403 (mtm) REVERT: A 456 MET cc_start: 0.9335 (mmp) cc_final: 0.8260 (mmm) REVERT: A 482 PHE cc_start: 0.8777 (m-80) cc_final: 0.8399 (m-80) REVERT: A 748 MET cc_start: 0.9397 (ttp) cc_final: 0.8936 (ptm) REVERT: A 818 MET cc_start: 0.9451 (mtt) cc_final: 0.9222 (mmt) REVERT: A 873 MET cc_start: 0.9322 (mmp) cc_final: 0.8801 (mmm) REVERT: A 1209 MET cc_start: 0.8920 (mmm) cc_final: 0.7973 (mmm) REVERT: A 1265 ASN cc_start: 0.9213 (m110) cc_final: 0.8970 (m-40) REVERT: A 1285 MET cc_start: 0.9268 (tpt) cc_final: 0.8917 (tpp) REVERT: A 1368 MET cc_start: 0.8708 (mtm) cc_final: 0.8487 (mtm) REVERT: A 1376 THR cc_start: 0.9555 (m) cc_final: 0.8897 (m) REVERT: A 1433 MET cc_start: 0.9076 (tpt) cc_final: 0.8717 (tpp) REVERT: B 92 PHE cc_start: 0.9413 (m-80) cc_final: 0.9150 (m-80) REVERT: B 199 MET cc_start: 0.8192 (tpt) cc_final: 0.7438 (tpt) REVERT: B 417 PHE cc_start: 0.9306 (t80) cc_final: 0.8876 (t80) REVERT: B 432 MET cc_start: 0.9337 (ptp) cc_final: 0.9011 (ptp) REVERT: B 438 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8887 (pt0) REVERT: B 552 MET cc_start: 0.9462 (tpp) cc_final: 0.9189 (tpp) REVERT: B 637 LEU cc_start: 0.9188 (tp) cc_final: 0.8712 (tp) REVERT: B 698 GLU cc_start: 0.9397 (tt0) cc_final: 0.9175 (tt0) REVERT: B 747 MET cc_start: 0.9109 (mmm) cc_final: 0.8632 (tmm) REVERT: B 773 MET cc_start: 0.9148 (mtm) cc_final: 0.8810 (mtt) REVERT: B 778 MET cc_start: 0.8420 (mmp) cc_final: 0.7764 (tpp) REVERT: B 789 MET cc_start: 0.9232 (mmm) cc_final: 0.8934 (mmm) REVERT: B 841 MET cc_start: 0.9026 (ttm) cc_final: 0.8764 (tpp) REVERT: B 861 ASP cc_start: 0.8462 (t0) cc_final: 0.8241 (t70) REVERT: B 1009 ASP cc_start: 0.8611 (m-30) cc_final: 0.8354 (m-30) REVERT: B 1082 MET cc_start: 0.8538 (tpt) cc_final: 0.8211 (tpp) REVERT: B 1092 TYR cc_start: 0.9172 (m-80) cc_final: 0.8897 (m-80) REVERT: B 1111 MET cc_start: 0.8976 (mmm) cc_final: 0.8365 (mmm) REVERT: B 1132 GLU cc_start: 0.8989 (pp20) cc_final: 0.8632 (pp20) REVERT: B 1136 ASP cc_start: 0.9352 (m-30) cc_final: 0.8954 (m-30) REVERT: B 1138 MET cc_start: 0.9557 (mmm) cc_final: 0.9146 (mmm) REVERT: B 1208 MET cc_start: 0.9421 (mtp) cc_final: 0.9041 (mtm) REVERT: E 22 MET cc_start: 0.9345 (ppp) cc_final: 0.9101 (ppp) REVERT: E 57 MET cc_start: 0.8704 (ptt) cc_final: 0.8352 (mpp) REVERT: E 58 MET cc_start: 0.8268 (mtm) cc_final: 0.8046 (mtt) REVERT: E 82 PHE cc_start: 0.8462 (m-80) cc_final: 0.7717 (m-80) REVERT: E 93 MET cc_start: 0.9347 (tmm) cc_final: 0.9115 (tmm) REVERT: E 182 ASP cc_start: 0.9213 (t0) cc_final: 0.8849 (t0) REVERT: F 97 ARG cc_start: 0.9673 (tpm170) cc_final: 0.9263 (tpm170) REVERT: F 100 GLN cc_start: 0.9678 (mp10) cc_final: 0.9242 (mp10) REVERT: G 22 MET cc_start: 0.9559 (ptp) cc_final: 0.9188 (ptm) REVERT: G 25 TYR cc_start: 0.9569 (m-80) cc_final: 0.9027 (m-80) REVERT: G 44 TYR cc_start: 0.8643 (m-10) cc_final: 0.8390 (m-10) REVERT: G 88 ASP cc_start: 0.7225 (m-30) cc_final: 0.6754 (m-30) REVERT: G 115 MET cc_start: 0.5254 (mmm) cc_final: 0.4857 (mmm) REVERT: G 166 ASP cc_start: 0.8138 (t0) cc_final: 0.7854 (t0) REVERT: H 40 LEU cc_start: 0.9493 (tp) cc_final: 0.9223 (tt) REVERT: H 97 MET cc_start: 0.9017 (mtp) cc_final: 0.8747 (mtp) REVERT: H 142 LEU cc_start: 0.9656 (tp) cc_final: 0.9132 (tp) REVERT: I 47 GLU cc_start: 0.9294 (tt0) cc_final: 0.8990 (tt0) REVERT: I 86 PHE cc_start: 0.9449 (p90) cc_final: 0.9179 (p90) REVERT: J 49 MET cc_start: 0.9357 (mmp) cc_final: 0.8640 (mmm) REVERT: K 50 LEU cc_start: 0.9515 (mt) cc_final: 0.9289 (mt) REVERT: K 85 ASP cc_start: 0.9107 (m-30) cc_final: 0.8714 (t70) REVERT: L 64 LEU cc_start: 0.8465 (mt) cc_final: 0.8262 (mt) REVERT: L 68 GLU cc_start: 0.8741 (tt0) cc_final: 0.8266 (tm-30) REVERT: M 55 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8423 (mtmt) REVERT: Q 336 ASP cc_start: 0.6894 (t70) cc_final: 0.6514 (t0) REVERT: R 274 ASN cc_start: 0.9223 (t0) cc_final: 0.8932 (p0) REVERT: U 244 MET cc_start: 0.9268 (ttp) cc_final: 0.9033 (ttm) outliers start: 3 outliers final: 1 residues processed: 468 average time/residue: 0.2311 time to fit residues: 182.2024 Evaluate side-chains 375 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 196 optimal weight: 8.9990 chunk 475 optimal weight: 30.0000 chunk 511 optimal weight: 40.0000 chunk 443 optimal weight: 6.9990 chunk 453 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 472 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A1009 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN C 79 GLN D 51 ASN D 173 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** M 127 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 = 0.3297 r_free = 0.3297 target = 0.052066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038611 restraints weight = 335536.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.039741 restraints weight = 198195.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040564 restraints weight = 137019.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.041121 restraints weight = 104712.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.041474 restraints weight = 86489.162| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 42618 Z= 0.210 Angle : 0.706 26.712 57836 Z= 0.360 Chirality : 0.044 0.276 6559 Planarity : 0.005 0.095 7176 Dihedral : 14.353 100.916 6560 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.86 % Favored : 93.88 % Rotamer: Outliers : 0.02 % Allowed : 1.79 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.12), residues: 5066 helix: 0.96 (0.12), residues: 1970 sheet: -0.69 (0.17), residues: 884 loop : -0.88 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 153 TYR 0.020 0.002 TYR B1091 PHE 0.035 0.002 PHE B 226 TRP 0.020 0.002 TRP U 42 HIS 0.008 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (42582) covalent geometry : angle 0.66649 / 0.36 (57791) hydrogen bonds : bond 0.04148 / 2.80 ( 1919) hydrogen bonds : angle 5.40293 / 3.79 ( 5437) metal coordination : bond 0.01479 / 0.80 ( 35) metal coordination : angle 8.42192 / 5.40 ( 45) Misc. bond : bond 0.00026 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 468 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9402 (tp30) cc_final: 0.9188 (pp20) REVERT: A 122 MET cc_start: 0.9012 (mtp) cc_final: 0.8735 (mtp) REVERT: A 290 GLU cc_start: 0.9619 (pt0) cc_final: 0.9414 (pt0) REVERT: A 340 LEU cc_start: 0.9803 (mt) cc_final: 0.9470 (mt) REVERT: A 341 MET cc_start: 0.8678 (mmt) cc_final: 0.7707 (mmt) REVERT: A 431 LYS cc_start: 0.9505 (mppt) cc_final: 0.9116 (mmtm) REVERT: A 452 LYS cc_start: 0.8963 (tttm) cc_final: 0.8531 (tptp) REVERT: A 453 MET cc_start: 0.9724 (pmm) cc_final: 0.9289 (pmm) REVERT: A 455 MET cc_start: 0.9232 (mtm) cc_final: 0.8684 (ptp) REVERT: A 456 MET cc_start: 0.9273 (mmp) cc_final: 0.8285 (mmm) REVERT: A 487 MET cc_start: 0.8566 (mtp) cc_final: 0.8039 (mtp) REVERT: A 521 MET cc_start: 0.9228 (mmp) cc_final: 0.8565 (mmm) REVERT: A 546 VAL cc_start: 0.9568 (t) cc_final: 0.9231 (t) REVERT: A 549 MET cc_start: 0.9563 (mtt) cc_final: 0.9051 (mpp) REVERT: A 748 MET cc_start: 0.9372 (ttp) cc_final: 0.8979 (ptm) REVERT: A 761 MET cc_start: 0.8941 (mpp) cc_final: 0.8710 (mpp) REVERT: A 818 MET cc_start: 0.9439 (mtt) cc_final: 0.9142 (mmt) REVERT: A 873 MET cc_start: 0.9282 (mmp) cc_final: 0.8744 (mmm) REVERT: A 1209 MET cc_start: 0.8814 (mmm) cc_final: 0.7855 (mmm) REVERT: A 1265 ASN cc_start: 0.9202 (m110) cc_final: 0.8953 (m-40) REVERT: A 1267 MET cc_start: 0.9459 (ptp) cc_final: 0.9217 (ptt) REVERT: A 1285 MET cc_start: 0.9255 (tpt) cc_final: 0.8906 (tpp) REVERT: A 1368 MET cc_start: 0.8769 (mtm) cc_final: 0.8547 (mtm) REVERT: A 1376 THR cc_start: 0.9534 (m) cc_final: 0.8868 (m) REVERT: A 1433 MET cc_start: 0.9083 (tpt) cc_final: 0.8735 (tpp) REVERT: B 92 PHE cc_start: 0.9416 (m-80) cc_final: 0.9208 (m-80) REVERT: B 199 MET cc_start: 0.8130 (tpt) cc_final: 0.7379 (tpt) REVERT: B 400 HIS cc_start: 0.9386 (t-90) cc_final: 0.9154 (t-90) REVERT: B 417 PHE cc_start: 0.9287 (t80) cc_final: 0.8907 (t80) REVERT: B 432 MET cc_start: 0.9332 (ptp) cc_final: 0.8940 (ptp) REVERT: B 542 MET cc_start: 0.8627 (tpp) cc_final: 0.8353 (tpp) REVERT: B 552 MET cc_start: 0.9448 (tpp) cc_final: 0.9119 (tpp) REVERT: B 615 MET cc_start: 0.7431 (ptt) cc_final: 0.7199 (ptt) REVERT: B 637 LEU cc_start: 0.9151 (tp) cc_final: 0.8654 (tp) REVERT: B 773 MET cc_start: 0.9169 (mtm) cc_final: 0.8806 (mtt) REVERT: B 778 MET cc_start: 0.8449 (mmp) cc_final: 0.7741 (tpp) REVERT: B 789 MET cc_start: 0.9208 (mmm) cc_final: 0.8911 (mmm) REVERT: B 1082 MET cc_start: 0.8561 (tpt) cc_final: 0.8190 (tpp) REVERT: B 1093 GLN cc_start: 0.8788 (mp10) cc_final: 0.8571 (pm20) REVERT: B 1111 MET cc_start: 0.8949 (mmm) cc_final: 0.8118 (mmp) REVERT: B 1132 GLU cc_start: 0.8993 (pp20) cc_final: 0.8668 (pp20) REVERT: B 1133 MET cc_start: 0.9300 (mtp) cc_final: 0.8976 (ttm) REVERT: B 1136 ASP cc_start: 0.9298 (m-30) cc_final: 0.8869 (m-30) REVERT: B 1208 MET cc_start: 0.9384 (mtp) cc_final: 0.9021 (mtm) REVERT: B 1210 MET cc_start: 0.9320 (mmp) cc_final: 0.8828 (mmm) REVERT: C 33 LEU cc_start: 0.9678 (mm) cc_final: 0.9333 (mm) REVERT: E 22 MET cc_start: 0.9332 (ppp) cc_final: 0.9081 (ppp) REVERT: E 57 MET cc_start: 0.8728 (ptt) cc_final: 0.8336 (mpp) REVERT: E 58 MET cc_start: 0.8203 (mtm) cc_final: 0.7988 (mtt) REVERT: E 82 PHE cc_start: 0.8475 (m-80) cc_final: 0.7724 (m-80) REVERT: E 93 MET cc_start: 0.9366 (tmm) cc_final: 0.9124 (tmm) REVERT: E 112 TYR cc_start: 0.9404 (p90) cc_final: 0.8228 (p90) REVERT: E 182 ASP cc_start: 0.9202 (t0) cc_final: 0.8856 (t0) REVERT: F 85 MET cc_start: 0.8628 (tmm) cc_final: 0.8325 (tmm) REVERT: F 97 ARG cc_start: 0.9663 (tpm170) cc_final: 0.9402 (tpm170) REVERT: F 100 GLN cc_start: 0.9607 (mp10) cc_final: 0.9373 (mm-40) REVERT: G 22 MET cc_start: 0.9597 (ptp) cc_final: 0.9227 (ptm) REVERT: G 25 TYR cc_start: 0.9572 (m-80) cc_final: 0.9047 (m-80) REVERT: G 44 TYR cc_start: 0.8626 (m-10) cc_final: 0.8357 (m-10) REVERT: G 88 ASP cc_start: 0.7162 (m-30) cc_final: 0.6682 (m-30) REVERT: G 115 MET cc_start: 0.5618 (mmm) cc_final: 0.5098 (mmm) REVERT: G 166 ASP cc_start: 0.8212 (t0) cc_final: 0.7909 (t0) REVERT: H 40 LEU cc_start: 0.9502 (tp) cc_final: 0.9240 (tt) REVERT: H 97 MET cc_start: 0.8960 (mtp) cc_final: 0.8567 (mtp) REVERT: H 142 LEU cc_start: 0.9666 (tp) cc_final: 0.9149 (tp) REVERT: I 47 GLU cc_start: 0.9299 (tt0) cc_final: 0.9011 (tt0) REVERT: I 86 PHE cc_start: 0.9441 (p90) cc_final: 0.9142 (p90) REVERT: J 49 MET cc_start: 0.9329 (mmp) cc_final: 0.8580 (mmm) REVERT: K 50 LEU cc_start: 0.9499 (mt) cc_final: 0.9297 (mt) REVERT: K 67 PHE cc_start: 0.9028 (m-80) cc_final: 0.8719 (m-80) REVERT: K 85 ASP cc_start: 0.9015 (m-30) cc_final: 0.8614 (t70) REVERT: L 64 LEU cc_start: 0.8493 (mt) cc_final: 0.8266 (mt) REVERT: L 68 GLU cc_start: 0.8788 (tt0) cc_final: 0.8512 (tm-30) REVERT: Q 344 PHE cc_start: 0.9235 (t80) cc_final: 0.9015 (t80) REVERT: Q 376 LEU cc_start: 0.8963 (tt) cc_final: 0.8540 (tt) REVERT: Q 386 MET cc_start: 0.6295 (mpp) cc_final: 0.5679 (mmp) REVERT: R 274 ASN cc_start: 0.9236 (t0) cc_final: 0.8941 (p0) REVERT: U 244 MET cc_start: 0.9278 (ttp) cc_final: 0.8977 (ttm) REVERT: U 262 LEU cc_start: 0.8573 (mt) cc_final: 0.8175 (mp) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.2296 time to fit residues: 181.8960 Evaluate side-chains 366 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 5 optimal weight: 0.0020 chunk 372 optimal weight: 0.2980 chunk 376 optimal weight: 6.9990 chunk 409 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 377 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 452 optimal weight: 20.0000 chunk 368 optimal weight: 5.9990 overall best weight: 4.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN C 79 GLN D 173 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.051826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038496 restraints weight = 335825.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.039620 restraints weight = 200295.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.040398 restraints weight = 139158.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.040943 restraints weight = 107745.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.041234 restraints weight = 88707.247| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 42618 Z= 0.204 Angle : 0.697 24.494 57836 Z= 0.355 Chirality : 0.044 0.263 6559 Planarity : 0.005 0.066 7176 Dihedral : 14.291 98.799 6560 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.22 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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 are not related in a simple way. whole: -0.19 (0.12), residues: 5066 helix: 1.04 (0.12), residues: 1969 sheet: -0.72 (0.17), residues: 881 loop : -0.88 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1055 TYR 0.019 0.002 TYR F 84 PHE 0.032 0.002 PHE D 70 TRP 0.035 0.002 TRP U 42 HIS 0.014 0.002 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (42582) covalent geometry : angle 0.66019 / 0.35 (57791) hydrogen bonds : bond 0.04096 / 2.75 ( 1919) hydrogen bonds : angle 5.37091 / 3.77 ( 5437) metal coordination : bond 0.01424 / 0.77 ( 35) metal coordination : angle 8.06603 / 5.13 ( 45) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9352 (tp30) cc_final: 0.9077 (pp20) REVERT: A 88 LYS cc_start: 0.9385 (tmmt) cc_final: 0.9052 (tmtt) REVERT: A 122 MET cc_start: 0.8992 (mtp) cc_final: 0.8747 (mtp) REVERT: A 290 GLU cc_start: 0.9610 (pt0) cc_final: 0.9405 (pt0) REVERT: A 330 LYS cc_start: 0.8993 (tttt) cc_final: 0.8514 (ptpp) REVERT: A 340 LEU cc_start: 0.9774 (mt) cc_final: 0.9407 (mt) REVERT: A 341 MET cc_start: 0.8623 (mmt) cc_final: 0.7772 (mmt) REVERT: A 431 LYS cc_start: 0.9523 (mppt) cc_final: 0.9137 (mmtm) REVERT: A 453 MET cc_start: 0.9707 (pmm) cc_final: 0.9282 (pmm) REVERT: A 455 MET cc_start: 0.9076 (mtm) cc_final: 0.8660 (ptp) REVERT: A 456 MET cc_start: 0.9306 (mmp) cc_final: 0.8387 (mmm) REVERT: A 521 MET cc_start: 0.9322 (mmp) cc_final: 0.8713 (mmm) REVERT: A 546 VAL cc_start: 0.9549 (t) cc_final: 0.9228 (t) REVERT: A 549 MET cc_start: 0.9523 (mtt) cc_final: 0.9072 (mpp) REVERT: A 748 MET cc_start: 0.9358 (ttp) cc_final: 0.9022 (ptm) REVERT: A 761 MET cc_start: 0.8891 (mpp) cc_final: 0.8652 (mpp) REVERT: A 818 MET cc_start: 0.9425 (mtt) cc_final: 0.9018 (mmt) REVERT: A 873 MET cc_start: 0.9239 (mmp) cc_final: 0.8920 (mmp) REVERT: A 1209 MET cc_start: 0.8936 (mmm) cc_final: 0.7858 (mmm) REVERT: A 1265 ASN cc_start: 0.9200 (m110) cc_final: 0.8951 (m-40) REVERT: A 1285 MET cc_start: 0.9176 (tpt) cc_final: 0.8807 (tpp) REVERT: A 1376 THR cc_start: 0.9525 (m) cc_final: 0.8880 (m) REVERT: A 1433 MET cc_start: 0.9073 (tpt) cc_final: 0.8745 (tpp) REVERT: B 92 PHE cc_start: 0.9368 (m-80) cc_final: 0.9158 (m-80) REVERT: B 199 MET cc_start: 0.8092 (tpt) cc_final: 0.7360 (tpt) REVERT: B 400 HIS cc_start: 0.9383 (t-90) cc_final: 0.9090 (t-90) REVERT: B 417 PHE cc_start: 0.9268 (t80) cc_final: 0.8878 (t80) REVERT: B 432 MET cc_start: 0.9338 (ptp) cc_final: 0.8928 (ptp) REVERT: B 552 MET cc_start: 0.9429 (tpp) cc_final: 0.9122 (tpp) REVERT: B 637 LEU cc_start: 0.9134 (tp) cc_final: 0.8652 (tp) REVERT: B 698 GLU cc_start: 0.9362 (tt0) cc_final: 0.9119 (tt0) REVERT: B 747 MET cc_start: 0.9012 (mmm) cc_final: 0.8749 (tpp) REVERT: B 773 MET cc_start: 0.9141 (mtm) cc_final: 0.8785 (mtt) REVERT: B 841 MET cc_start: 0.9006 (tpt) cc_final: 0.8767 (tpp) REVERT: B 1009 ASP cc_start: 0.8802 (m-30) cc_final: 0.8358 (m-30) REVERT: B 1082 MET cc_start: 0.8472 (tpt) cc_final: 0.8055 (tpp) REVERT: B 1093 GLN cc_start: 0.8837 (mp10) cc_final: 0.8545 (mp10) REVERT: B 1132 GLU cc_start: 0.9035 (pp20) cc_final: 0.8435 (pp20) REVERT: B 1133 MET cc_start: 0.9222 (mtp) cc_final: 0.8646 (ttm) REVERT: B 1136 ASP cc_start: 0.9301 (m-30) cc_final: 0.8425 (m-30) REVERT: B 1138 MET cc_start: 0.9536 (mmm) cc_final: 0.9293 (tpp) REVERT: B 1170 THR cc_start: 0.9413 (m) cc_final: 0.9034 (p) REVERT: B 1208 MET cc_start: 0.9364 (mtp) cc_final: 0.9014 (mtm) REVERT: B 1210 MET cc_start: 0.9341 (mmp) cc_final: 0.8924 (mmm) REVERT: C 33 LEU cc_start: 0.9693 (mm) cc_final: 0.9442 (mm) REVERT: C 37 MET cc_start: 0.9069 (mpp) cc_final: 0.8746 (mmm) REVERT: E 22 MET cc_start: 0.9326 (ppp) cc_final: 0.9053 (ppp) REVERT: E 57 MET cc_start: 0.8677 (ptt) cc_final: 0.8316 (mpp) REVERT: E 82 PHE cc_start: 0.8497 (m-80) cc_final: 0.7754 (m-80) REVERT: E 112 TYR cc_start: 0.9403 (p90) cc_final: 0.8212 (p90) REVERT: E 178 ILE cc_start: 0.9446 (tt) cc_final: 0.9009 (tt) REVERT: E 182 ASP cc_start: 0.9217 (t0) cc_final: 0.8840 (t0) REVERT: F 84 TYR cc_start: 0.9038 (m-80) cc_final: 0.8835 (m-80) REVERT: F 85 MET cc_start: 0.8587 (tmm) cc_final: 0.8283 (tmm) REVERT: F 97 ARG cc_start: 0.9642 (tpm170) cc_final: 0.9394 (tpm170) REVERT: F 100 GLN cc_start: 0.9603 (mp10) cc_final: 0.9274 (mm-40) REVERT: G 25 TYR cc_start: 0.9550 (m-80) cc_final: 0.9050 (m-80) REVERT: G 44 TYR cc_start: 0.8602 (m-10) cc_final: 0.8307 (m-10) REVERT: G 88 ASP cc_start: 0.7157 (m-30) cc_final: 0.6657 (m-30) REVERT: G 115 MET cc_start: 0.5740 (mmm) cc_final: 0.5225 (mmm) REVERT: G 166 ASP cc_start: 0.8350 (t0) cc_final: 0.8063 (t0) REVERT: H 40 LEU cc_start: 0.9500 (tp) cc_final: 0.9229 (tt) REVERT: H 97 MET cc_start: 0.8856 (mtp) cc_final: 0.8566 (mtp) REVERT: H 142 LEU cc_start: 0.9640 (tp) cc_final: 0.9127 (tp) REVERT: J 49 MET cc_start: 0.9314 (mmp) cc_final: 0.8601 (mmm) REVERT: K 50 LEU cc_start: 0.9506 (mt) cc_final: 0.9262 (mt) REVERT: K 85 ASP cc_start: 0.8968 (m-30) cc_final: 0.8591 (t70) REVERT: L 64 LEU cc_start: 0.8493 (mt) cc_final: 0.8259 (mt) REVERT: M 55 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8243 (mtmt) REVERT: M 148 ASP cc_start: 0.9652 (m-30) cc_final: 0.9011 (p0) REVERT: Q 386 MET cc_start: 0.6260 (mpp) cc_final: 0.5653 (mmm) REVERT: R 274 ASN cc_start: 0.9256 (t0) cc_final: 0.8943 (p0) REVERT: U 244 MET cc_start: 0.9249 (ttp) cc_final: 0.8929 (ttm) REVERT: U 262 LEU cc_start: 0.8588 (mt) cc_final: 0.8191 (mp) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.2293 time to fit residues: 175.2708 Evaluate side-chains 362 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 304 optimal weight: 0.7980 chunk 265 optimal weight: 10.0000 chunk 374 optimal weight: 0.7980 chunk 344 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 493 optimal weight: 30.0000 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 GLN ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.052151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.038781 restraints weight = 329173.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039909 restraints weight = 197098.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040652 restraints weight = 137368.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041256 restraints weight = 107019.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041513 restraints weight = 87708.021| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 42618 Z= 0.163 Angle : 0.685 22.631 57836 Z= 0.349 Chirality : 0.044 0.238 6559 Planarity : 0.004 0.071 7176 Dihedral : 14.213 97.150 6560 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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 are not related in a simple way. whole: -0.10 (0.12), residues: 5066 helix: 1.15 (0.12), residues: 1969 sheet: -0.71 (0.17), residues: 880 loop : -0.84 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1055 TYR 0.019 0.002 TYR E 211 PHE 0.027 0.002 PHE M 189 TRP 0.032 0.002 TRP U 42 HIS 0.008 0.001 HIS M 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (42582) covalent geometry : angle 0.65065 / 0.35 (57791) hydrogen bonds : bond 0.03850 / 2.58 ( 1919) hydrogen bonds : angle 5.31267 / 3.73 ( 5437) metal coordination : bond 0.01207 / 0.63 ( 35) metal coordination : angle 7.70518 / 4.81 ( 45) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9395 (tmmt) cc_final: 0.9070 (tmtt) REVERT: A 122 MET cc_start: 0.9051 (mtp) cc_final: 0.8809 (mtp) REVERT: A 234 MET cc_start: 0.9582 (ttm) cc_final: 0.9360 (ttm) REVERT: A 290 GLU cc_start: 0.9611 (pt0) cc_final: 0.9411 (pt0) REVERT: A 340 LEU cc_start: 0.9782 (mt) cc_final: 0.9407 (mt) REVERT: A 341 MET cc_start: 0.8588 (mmt) cc_final: 0.7572 (mmt) REVERT: A 353 ILE cc_start: 0.9589 (pt) cc_final: 0.9359 (pt) REVERT: A 453 MET cc_start: 0.9699 (pmm) cc_final: 0.9408 (pmm) REVERT: A 455 MET cc_start: 0.9026 (mtm) cc_final: 0.8782 (ptp) REVERT: A 456 MET cc_start: 0.9222 (mmp) cc_final: 0.8412 (mmm) REVERT: A 469 ARG cc_start: 0.9414 (mmt90) cc_final: 0.9138 (mmm-85) REVERT: A 487 MET cc_start: 0.8668 (mtp) cc_final: 0.8391 (mtp) REVERT: A 521 MET cc_start: 0.9383 (mmp) cc_final: 0.8718 (mmm) REVERT: A 546 VAL cc_start: 0.9580 (t) cc_final: 0.9289 (t) REVERT: A 549 MET cc_start: 0.9514 (mtt) cc_final: 0.9048 (mpp) REVERT: A 748 MET cc_start: 0.9392 (ttp) cc_final: 0.9056 (ptm) REVERT: A 761 MET cc_start: 0.8928 (mpp) cc_final: 0.8623 (mpp) REVERT: A 818 MET cc_start: 0.9367 (mtt) cc_final: 0.9109 (mmm) REVERT: A 873 MET cc_start: 0.9210 (mmp) cc_final: 0.8840 (mmm) REVERT: A 1209 MET cc_start: 0.8841 (mmm) cc_final: 0.7869 (mmm) REVERT: A 1265 ASN cc_start: 0.9216 (m110) cc_final: 0.8969 (m-40) REVERT: A 1368 MET cc_start: 0.8852 (mtp) cc_final: 0.8344 (mtt) REVERT: A 1376 THR cc_start: 0.9460 (m) cc_final: 0.8789 (m) REVERT: A 1433 MET cc_start: 0.9061 (tpt) cc_final: 0.8730 (tpp) REVERT: B 92 PHE cc_start: 0.9356 (m-80) cc_final: 0.9100 (m-80) REVERT: B 417 PHE cc_start: 0.9245 (t80) cc_final: 0.8859 (t80) REVERT: B 421 PHE cc_start: 0.9303 (t80) cc_final: 0.9101 (t80) REVERT: B 432 MET cc_start: 0.9409 (ptp) cc_final: 0.8986 (ptp) REVERT: B 438 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8870 (pt0) REVERT: B 552 MET cc_start: 0.9400 (tpp) cc_final: 0.9047 (tpp) REVERT: B 637 LEU cc_start: 0.8844 (tp) cc_final: 0.8596 (tp) REVERT: B 698 GLU cc_start: 0.9348 (tt0) cc_final: 0.9147 (tm-30) REVERT: B 747 MET cc_start: 0.9046 (mmm) cc_final: 0.8749 (tpp) REVERT: B 773 MET cc_start: 0.9204 (mtm) cc_final: 0.8812 (mtt) REVERT: B 789 MET cc_start: 0.9108 (mmm) cc_final: 0.8853 (mmm) REVERT: B 841 MET cc_start: 0.9082 (tpt) cc_final: 0.8874 (tpp) REVERT: B 1009 ASP cc_start: 0.8620 (m-30) cc_final: 0.8337 (m-30) REVERT: B 1082 MET cc_start: 0.8479 (tpt) cc_final: 0.8049 (tpp) REVERT: B 1093 GLN cc_start: 0.8793 (mp10) cc_final: 0.8453 (mp10) REVERT: B 1111 MET cc_start: 0.8953 (mmm) cc_final: 0.8518 (mmm) REVERT: B 1132 GLU cc_start: 0.9050 (pp20) cc_final: 0.8432 (pp20) REVERT: B 1133 MET cc_start: 0.9242 (mtp) cc_final: 0.8641 (ttm) REVERT: B 1136 ASP cc_start: 0.9288 (m-30) cc_final: 0.8413 (m-30) REVERT: B 1170 THR cc_start: 0.9414 (m) cc_final: 0.9041 (p) REVERT: B 1208 MET cc_start: 0.9359 (mtp) cc_final: 0.8995 (mtm) REVERT: B 1210 MET cc_start: 0.9331 (mmp) cc_final: 0.8938 (mmm) REVERT: C 33 LEU cc_start: 0.9605 (mm) cc_final: 0.9223 (mm) REVERT: E 22 MET cc_start: 0.9320 (ppp) cc_final: 0.9046 (ppp) REVERT: E 57 MET cc_start: 0.8802 (ptt) cc_final: 0.8427 (mpp) REVERT: E 58 MET cc_start: 0.8167 (mtm) cc_final: 0.7929 (mtt) REVERT: E 82 PHE cc_start: 0.8563 (m-80) cc_final: 0.7768 (m-80) REVERT: E 93 MET cc_start: 0.9360 (tmm) cc_final: 0.9067 (tmm) REVERT: E 112 TYR cc_start: 0.9398 (p90) cc_final: 0.8202 (p90) REVERT: E 182 ASP cc_start: 0.9192 (t0) cc_final: 0.8809 (t0) REVERT: E 211 TYR cc_start: 0.8999 (m-10) cc_final: 0.8784 (m-10) REVERT: F 84 TYR cc_start: 0.8979 (m-80) cc_final: 0.8760 (m-80) REVERT: F 85 MET cc_start: 0.8562 (tmm) cc_final: 0.8246 (tmm) REVERT: F 97 ARG cc_start: 0.9633 (tpm170) cc_final: 0.9291 (tpm170) REVERT: F 100 GLN cc_start: 0.9574 (mp10) cc_final: 0.9106 (mp10) REVERT: G 25 TYR cc_start: 0.9567 (m-80) cc_final: 0.9062 (m-80) REVERT: G 44 TYR cc_start: 0.8602 (m-10) cc_final: 0.8284 (m-10) REVERT: G 88 ASP cc_start: 0.7248 (m-30) cc_final: 0.6776 (m-30) REVERT: G 115 MET cc_start: 0.5909 (mmm) cc_final: 0.5388 (mmm) REVERT: G 166 ASP cc_start: 0.8394 (t0) cc_final: 0.8102 (t0) REVERT: H 40 LEU cc_start: 0.9494 (tp) cc_final: 0.9236 (tt) REVERT: H 97 MET cc_start: 0.8830 (mtp) cc_final: 0.8584 (mtp) REVERT: H 142 LEU cc_start: 0.9602 (tp) cc_final: 0.9088 (tp) REVERT: I 68 LEU cc_start: 0.9089 (tt) cc_final: 0.8785 (tt) REVERT: I 86 PHE cc_start: 0.9486 (p90) cc_final: 0.9216 (p90) REVERT: J 8 PHE cc_start: 0.9069 (m-80) cc_final: 0.8358 (m-80) REVERT: J 49 MET cc_start: 0.9321 (mmp) cc_final: 0.8499 (mmm) REVERT: K 22 ASP cc_start: 0.9422 (m-30) cc_final: 0.8601 (p0) REVERT: K 50 LEU cc_start: 0.9540 (mt) cc_final: 0.9318 (mt) REVERT: K 85 ASP cc_start: 0.8980 (m-30) cc_final: 0.8588 (t70) REVERT: L 64 LEU cc_start: 0.8479 (mt) cc_final: 0.8241 (mt) REVERT: M 148 ASP cc_start: 0.9636 (m-30) cc_final: 0.8995 (p0) REVERT: M 246 LEU cc_start: 0.9632 (mt) cc_final: 0.9418 (mp) REVERT: Q 386 MET cc_start: 0.6287 (mpp) cc_final: 0.5559 (mmm) REVERT: R 263 MET cc_start: 0.9512 (mmm) cc_final: 0.9231 (mmm) REVERT: R 274 ASN cc_start: 0.9256 (t0) cc_final: 0.9015 (p0) REVERT: U 244 MET cc_start: 0.9267 (ttp) cc_final: 0.8972 (ttm) REVERT: V 78 PHE cc_start: 0.9075 (m-10) cc_final: 0.8622 (m-80) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.2340 time to fit residues: 184.0848 Evaluate side-chains 364 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 393 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 271 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 466 optimal weight: 40.0000 chunk 3 optimal weight: 1.9990 chunk 419 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 204 optimal weight: 0.0370 chunk 487 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 overall best weight: 3.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN A 439 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 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 = 0.3296 r_free = 0.3296 target = 0.052055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.038615 restraints weight = 340589.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.039740 restraints weight = 202623.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.040487 restraints weight = 141834.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.041113 restraints weight = 110011.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041310 restraints weight = 89831.683| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 42618 Z= 0.172 Angle : 0.688 26.506 57836 Z= 0.348 Chirality : 0.043 0.265 6559 Planarity : 0.005 0.066 7176 Dihedral : 14.200 95.215 6560 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.18 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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 are not related in a simple way. whole: -0.07 (0.12), residues: 5066 helix: 1.18 (0.12), residues: 1968 sheet: -0.64 (0.17), residues: 864 loop : -0.85 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1055 TYR 0.015 0.002 TYR A 465 PHE 0.021 0.002 PHE U 25 TRP 0.044 0.002 TRP U 42 HIS 0.008 0.001 HIS M 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (42582) covalent geometry : angle 0.65100 / 0.35 (57791) hydrogen bonds : bond 0.03863 / 2.60 ( 1919) hydrogen bonds : angle 5.28580 / 3.71 ( 5437) metal coordination : bond 0.01168 / 0.62 ( 35) metal coordination : angle 7.97750 / 4.95 ( 45) Misc. bond : bond 0.00040 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10132 Ramachandran restraints generated. 5066 Oldfield, 0 Emsley, 5066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8819 (ptm) cc_final: 0.8545 (ptm) REVERT: A 88 LYS cc_start: 0.9397 (tmmt) cc_final: 0.9085 (tmtt) REVERT: A 122 MET cc_start: 0.9076 (mtp) cc_final: 0.8823 (mtp) REVERT: A 290 GLU cc_start: 0.9568 (pt0) cc_final: 0.9341 (pt0) REVERT: A 340 LEU cc_start: 0.9763 (mt) cc_final: 0.9450 (mt) REVERT: A 341 MET cc_start: 0.8473 (mmt) cc_final: 0.7497 (mmt) REVERT: A 452 LYS cc_start: 0.8892 (tttm) cc_final: 0.8659 (tptp) REVERT: A 453 MET cc_start: 0.9718 (pmm) cc_final: 0.9475 (pmm) REVERT: A 456 MET cc_start: 0.9205 (mmp) cc_final: 0.8453 (mmm) REVERT: A 521 MET cc_start: 0.9351 (mmp) cc_final: 0.8779 (mmm) REVERT: A 748 MET cc_start: 0.9349 (ttp) cc_final: 0.9053 (ptm) REVERT: A 761 MET cc_start: 0.8901 (mpp) cc_final: 0.8582 (mpp) REVERT: A 818 MET cc_start: 0.9273 (mtt) cc_final: 0.8978 (mmm) REVERT: A 845 LEU cc_start: 0.9595 (mt) cc_final: 0.9369 (mt) REVERT: A 873 MET cc_start: 0.9168 (mmp) cc_final: 0.8917 (mmp) REVERT: A 1209 MET cc_start: 0.8796 (mmm) cc_final: 0.7639 (mmm) REVERT: A 1265 ASN cc_start: 0.9238 (m110) cc_final: 0.9009 (m-40) REVERT: A 1368 MET cc_start: 0.8785 (mtp) cc_final: 0.8276 (mtt) REVERT: A 1374 VAL cc_start: 0.9677 (p) cc_final: 0.9419 (m) REVERT: A 1376 THR cc_start: 0.9421 (m) cc_final: 0.8744 (m) REVERT: A 1433 MET cc_start: 0.9095 (tpt) cc_final: 0.8747 (tpp) REVERT: B 199 MET cc_start: 0.8121 (tpt) cc_final: 0.7248 (tpt) REVERT: B 417 PHE cc_start: 0.9228 (t80) cc_final: 0.8899 (t80) REVERT: B 438 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8855 (mt-10) REVERT: B 552 MET cc_start: 0.9357 (tpp) cc_final: 0.9031 (tpp) REVERT: B 637 LEU cc_start: 0.8937 (tp) cc_final: 0.8707 (tp) REVERT: B 747 MET cc_start: 0.9011 (mmm) cc_final: 0.8805 (tpp) REVERT: B 773 MET cc_start: 0.9130 (mtm) cc_final: 0.8744 (mtt) REVERT: B 778 MET cc_start: 0.8113 (mmp) cc_final: 0.7823 (tpp) REVERT: B 789 MET cc_start: 0.9088 (mmm) cc_final: 0.8834 (mmm) REVERT: B 837 ASP cc_start: 0.7977 (t0) cc_final: 0.7767 (t70) REVERT: B 841 MET cc_start: 0.9051 (tpt) cc_final: 0.8807 (tpp) REVERT: B 908 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7783 (tm-30) REVERT: B 1082 MET cc_start: 0.8472 (tpt) cc_final: 0.8028 (tpp) REVERT: B 1093 GLN cc_start: 0.8843 (mp10) cc_final: 0.8508 (mp10) REVERT: B 1111 MET cc_start: 0.8970 (mmm) cc_final: 0.8339 (mmm) REVERT: B 1132 GLU cc_start: 0.9057 (pp20) cc_final: 0.8354 (pp20) REVERT: B 1133 MET cc_start: 0.9224 (mtp) cc_final: 0.8619 (ttm) REVERT: B 1136 ASP cc_start: 0.9287 (m-30) cc_final: 0.8404 (m-30) REVERT: B 1138 MET cc_start: 0.9423 (mmm) cc_final: 0.9143 (tpt) REVERT: B 1170 THR cc_start: 0.9438 (m) cc_final: 0.9080 (p) REVERT: B 1208 MET cc_start: 0.9307 (mtp) cc_final: 0.9042 (ttm) REVERT: B 1210 MET cc_start: 0.9351 (mmp) cc_final: 0.8968 (mmm) REVERT: C 33 LEU cc_start: 0.9666 (mm) cc_final: 0.9272 (mm) REVERT: E 22 MET cc_start: 0.9311 (ppp) cc_final: 0.9027 (ppp) REVERT: E 57 MET cc_start: 0.8710 (ptt) cc_final: 0.8349 (mpp) REVERT: E 58 MET cc_start: 0.8096 (mtm) cc_final: 0.7839 (mtt) REVERT: E 82 PHE cc_start: 0.8359 (m-80) cc_final: 0.7675 (m-80) REVERT: E 93 MET cc_start: 0.9380 (tmm) cc_final: 0.9089 (tmm) REVERT: E 112 TYR cc_start: 0.9394 (p90) cc_final: 0.8188 (p90) REVERT: E 178 ILE cc_start: 0.9391 (tt) cc_final: 0.8969 (tt) REVERT: E 182 ASP cc_start: 0.9186 (t0) cc_final: 0.8811 (t0) REVERT: F 85 MET cc_start: 0.8499 (tmm) cc_final: 0.8278 (tmm) REVERT: F 97 ARG cc_start: 0.9615 (tpm170) cc_final: 0.9371 (tpm170) REVERT: F 100 GLN cc_start: 0.9592 (mp10) cc_final: 0.9347 (mm-40) REVERT: G 25 TYR cc_start: 0.9549 (m-80) cc_final: 0.9032 (m-80) REVERT: G 44 TYR cc_start: 0.8635 (m-10) cc_final: 0.8329 (m-10) REVERT: G 88 ASP cc_start: 0.7221 (m-30) cc_final: 0.6743 (m-30) REVERT: G 115 MET cc_start: 0.5952 (mmm) cc_final: 0.5418 (mmm) REVERT: G 166 ASP cc_start: 0.8443 (t0) cc_final: 0.8169 (t0) REVERT: H 40 LEU cc_start: 0.9490 (tp) cc_final: 0.9226 (tt) REVERT: H 142 LEU cc_start: 0.9586 (tp) cc_final: 0.9086 (tp) REVERT: I 68 LEU cc_start: 0.9032 (tt) cc_final: 0.8724 (tt) REVERT: I 86 PHE cc_start: 0.9479 (p90) cc_final: 0.9195 (p90) REVERT: J 8 PHE cc_start: 0.8986 (m-80) cc_final: 0.8214 (m-80) REVERT: J 49 MET cc_start: 0.9249 (mmp) cc_final: 0.8561 (mmm) REVERT: J 56 LEU cc_start: 0.9302 (mm) cc_final: 0.8987 (mm) REVERT: K 22 ASP cc_start: 0.9422 (m-30) cc_final: 0.8821 (m-30) REVERT: K 50 LEU cc_start: 0.9503 (mt) cc_final: 0.9288 (mt) REVERT: K 85 ASP cc_start: 0.8969 (m-30) cc_final: 0.8490 (t70) REVERT: L 64 LEU cc_start: 0.8522 (mt) cc_final: 0.8295 (mt) REVERT: M 135 MET cc_start: 0.9611 (pmm) cc_final: 0.9314 (pmm) REVERT: M 136 LEU cc_start: 0.9618 (mm) cc_final: 0.9404 (mm) REVERT: M 148 ASP cc_start: 0.9631 (m-30) cc_final: 0.8988 (p0) REVERT: M 246 LEU cc_start: 0.9630 (mt) cc_final: 0.9412 (mp) REVERT: R 274 ASN cc_start: 0.9295 (t0) cc_final: 0.9011 (p0) REVERT: U 244 MET cc_start: 0.9238 (ttp) cc_final: 0.8905 (ttm) REVERT: V 78 PHE cc_start: 0.9004 (m-10) cc_final: 0.8617 (m-80) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2374 time to fit residues: 181.3684 Evaluate side-chains 368 residues out of total 4585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 225 optimal weight: 5.9990 chunk 489 optimal weight: 4.9990 chunk 361 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 347 optimal weight: 0.0870 chunk 272 optimal weight: 0.9990 chunk 465 optimal weight: 50.0000 chunk 142 optimal weight: 8.9990 chunk 463 optimal weight: 50.0000 chunk 17 optimal weight: 20.0000 chunk 356 optimal weight: 20.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN B 465 ASN ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 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 = 0.3298 r_free = 0.3298 target = 0.052082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.038611 restraints weight = 344034.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.039788 restraints weight = 202954.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.040561 restraints weight = 140087.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.041040 restraints weight = 107798.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.041464 restraints weight = 90293.093| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 42618 Z= 0.166 Angle : 0.682 27.371 57836 Z= 0.345 Chirality : 0.043 0.226 6559 Planarity : 0.004 0.059 7176 Dihedral : 14.155 93.675 6560 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.14 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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 are not related in a simple way. whole: -0.00 (0.12), residues: 5066 helix: 1.25 (0.12), residues: 1960 sheet: -0.64 (0.17), residues: 830 loop : -0.81 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1055 TYR 0.020 0.001 TYR H 95 PHE 0.032 0.002 PHE D 70 TRP 0.045 0.002 TRP U 42 HIS 0.008 0.001 HIS M 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (42582) covalent geometry : angle 0.64628 / 0.34 (57791) hydrogen bonds : bond 0.03798 / 2.55 ( 1919) hydrogen bonds : angle 5.25601 / 3.69 ( 5437) metal coordination : bond 0.01270 / 0.65 ( 35) metal coordination : angle 7.81911 / 4.74 ( 45) Misc. bond : bond 0.00049 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6984.20 seconds wall clock time: 122 minutes 2.51 seconds (7322.51 seconds total)