Starting phenix.real_space_refine on Tue Aug 26 22:07:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gyl_0091/08_2025/6gyl_0091_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gyl_0091/08_2025/6gyl_0091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gyl_0091/08_2025/6gyl_0091_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gyl_0091/08_2025/6gyl_0091_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gyl_0091/08_2025/6gyl_0091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gyl_0091/08_2025/6gyl_0091.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 112 5.49 5 Mg 1 5.21 5 S 230 5.16 5 C 27071 2.51 5 N 7588 2.21 5 O 8397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43409 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: 9178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9178 Classifications: {'peptide': 1152} Link IDs: {'PTRANS': 51, 'TRANS': 1100} Chain breaks: 7 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: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2175 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 2 Chain: "N" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1129 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 9 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: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1303 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 6, 'HIS:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 4, 'ASN:plan1': 3, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 158 Chain: "T" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1149 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 9 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: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1469 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 182} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "X" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1004 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 7, 'TRANS': 152} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 9, 'TRP:plan': 2, 'GLU:plan': 6, 'TYR:plan': 6, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 158 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 90.335 128.252 128.144 1.00 0.00 S ATOM 837 SG CYS A 110 89.016 130.128 130.771 1.00 0.00 S ATOM 1142 SG CYS A 148 92.758 131.261 130.115 1.00 0.00 S ATOM 1211 SG CYS A 167 92.131 127.640 130.961 1.00 0.00 S ATOM 508 SG CYS A 67 49.090 121.848 103.505 1.00 0.00 S ATOM 530 SG CYS A 70 48.979 125.959 105.444 1.00 0.00 S ATOM 583 SG CYS A 77 50.583 124.457 101.901 1.00 0.00 S ATOM 19693 SG CYS B1163 53.771 136.633 114.926 1.00 0.00 S ATOM 19711 SG CYS B1166 57.635 134.486 114.489 1.00 0.00 S ATOM 19836 SG CYS B1182 54.251 132.763 113.861 1.00 0.00 S ATOM 19855 SG CYS B1185 54.921 134.164 116.994 1.00 0.00 S ATOM 20822 SG CYS C 86 23.864 128.122 40.062 1.00 0.00 S ATOM 20839 SG CYS C 88 24.580 125.308 42.115 1.00 0.00 S ATOM 20872 SG CYS C 92 24.456 125.123 38.621 1.00 0.00 S ATOM 20895 SG CYS C 95 27.578 126.406 39.453 1.00 0.00 S ATOM 28385 SG CYS I 7 143.345 110.639 85.304 1.00 0.00 S ATOM 28410 SG CYS I 10 141.267 107.799 87.542 1.00 0.00 S ATOM 28576 SG CYS I 29 141.130 111.997 87.933 1.00 0.00 S ATOM 28600 SG CYS I 32 143.874 109.861 88.665 1.00 0.00 S ATOM 28927 SG CYS I 75 134.628 130.777 45.585 1.00 0.00 S ATOM 28949 SG CYS I 78 135.146 128.000 42.825 1.00 0.00 S ATOM 29165 SG CYS I 103 132.166 127.298 44.291 1.00 0.00 S ATOM 29185 SG CYS I 106 135.744 126.804 46.204 1.00 0.00 S ATOM 29330 SG CYS J 7 59.178 129.901 32.220 1.00 0.00 S ATOM 29353 SG CYS J 10 57.669 132.031 29.929 1.00 0.00 S ATOM 29633 SG CYS J 45 60.981 133.567 30.316 1.00 0.00 S ATOM 29639 SG CYS J 46 59.816 130.465 28.489 1.00 0.00 S ATOM 30762 SG CYS L 31 54.372 90.589 53.582 1.00 0.00 S ATOM 30782 SG CYS L 34 53.510 88.753 50.615 1.00 0.00 S ATOM 30886 SG CYS L 48 52.642 88.314 54.892 1.00 0.00 S ATOM 30909 SG CYS L 51 55.898 87.634 53.758 1.00 0.00 S ATOM 31137 SG CYS M 24 28.773 126.975 87.662 1.00 0.00 S ATOM 31159 SG CYS M 27 26.541 126.178 85.730 1.00 0.00 S ATOM 31303 SG CYS M 45 29.463 124.143 84.323 1.00 0.00 S ATOM 31322 SG CYS M 48 28.298 128.317 84.550 1.00 0.00 S ATOM 41826 SG CYS W 124 35.061 114.115 116.841 1.00 0.00 S ATOM 41847 SG CYS W 127 37.745 114.885 114.702 1.00 0.00 S ATOM 42032 SG CYS W 149 35.318 117.715 115.408 1.00 0.00 S ATOM 42052 SG CYS W 152 34.656 114.547 112.818 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 92 residue: pdb=" P DT N 5 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT N 5 " occ=0.00 residue: pdb=" P DG N 6 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 6 " occ=0.00 residue: pdb=" P DC N 7 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 7 " occ=0.00 residue: pdb=" P DC N 8 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 8 " occ=0.00 residue: pdb=" P DC N 9 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 9 " occ=0.00 residue: pdb=" P DG N 10 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 10 " occ=0.00 residue: pdb=" P DG N 11 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 11 " occ=0.00 residue: pdb=" P DC N 12 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 12 " occ=0.00 residue: pdb=" P DC N 13 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 13 " occ=0.00 residue: pdb=" P DC N 14 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 14 " occ=0.00 residue: pdb=" P DA N 15 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 15 " occ=0.00 residue: pdb=" P DG N 16 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 16 " occ=0.00 ... (remaining 80 not shown) Time building chain proxies: 9.48, per 1000 atoms: 0.22 Number of scatterers: 43409 At special positions: 0 Unit cell: (165.9, 220.5, 168, 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 230 16.00 P 112 15.00 Mg 1 11.99 O 8397 8.00 N 7588 7.00 C 27071 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 Atom "ATOM 38901 O4' DA T 58 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb=" ZN W 601 " pdb="ZN ZN W 601 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 601 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 601 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 601 " - pdb=" SG CYS W 127 " Number of angles added : 57 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9914 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 59 sheets defined 41.0% alpha, 19.9% beta 46 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.653A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.641A pdb=" N ASN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.772A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.632A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.662A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.580A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.906A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.586A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.536A 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 637 removed outlier: 3.515A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 661 removed outlier: 4.116A pdb=" N VAL A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 646 " --> pdb=" O CYS A 642 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.615A pdb=" N LEU A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 removed outlier: 3.521A pdb=" N GLN A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 762 removed outlier: 3.711A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.982A pdb=" N PHE A 815 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 897 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.626A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.595A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 947 removed outlier: 3.599A pdb=" N GLN A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 3.727A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.665A pdb=" N ILE A 986 " --> pdb=" O THR A 982 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.543A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 3.616A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) Proline residue: A1075 - end of helix removed outlier: 4.002A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 removed outlier: 4.048A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.776A pdb=" N ALA A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.834A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 4.409A 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 1271 removed outlier: 4.303A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1319 removed outlier: 3.510A pdb=" N VAL A1316 " --> pdb=" O ASN A1312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1359 removed outlier: 3.703A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.861A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1403 removed outlier: 4.164A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1415 removed outlier: 3.530A pdb=" N ILE A1408 " --> pdb=" O GLU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1441 removed outlier: 3.935A pdb=" N PHE A1441 " --> pdb=" O THR A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1451 removed outlier: 3.606A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1446 through 1451' Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.880A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.106A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.841A 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 183 removed outlier: 3.719A pdb=" N SER B 182 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.762A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 324 removed outlier: 3.559A 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 Processing helix chain 'B' and resid 344 through 358 removed outlier: 3.872A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 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 removed outlier: 3.568A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.727A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.735A pdb=" N TRP B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 559 removed outlier: 3.585A pdb=" N SER B 559 " --> pdb=" O ILE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' 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 606 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.824A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.540A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.810A 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 removed outlier: 3.649A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.900A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 783 through 788 removed outlier: 4.213A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 removed outlier: 4.084A pdb=" N GLU B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (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: 4.361A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1039 removed outlier: 3.522A pdb=" N CYS B1029 " --> pdb=" O HIS B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.645A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1151 removed outlier: 3.744A 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 39 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 75 through 80 removed outlier: 4.287A pdb=" N GLU C 78 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) 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 removed outlier: 3.539A pdb=" N GLY C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.501A 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 removed outlier: 3.505A pdb=" N GLN C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 73 removed outlier: 3.720A pdb=" N LEU D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 132 removed outlier: 3.669A pdb=" N LEU D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.718A pdb=" N ALA D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.500A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.624A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.556A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.585A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS E 147 " --> pdb=" O ILE E 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 147' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.734A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.728A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.586A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.773A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.633A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 removed outlier: 3.794A pdb=" N GLY G 66 " --> pdb=" O PRO G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 66' Processing helix chain 'G' and resid 112 through 115 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.553A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 29 Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.696A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.176A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.782A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.521A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.770A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.600A pdb=" N ALA K 86 " --> pdb=" O ASP K 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 Processing helix chain 'M' and resid 85 through 89 Processing helix chain 'M' and resid 103 through 118 removed outlier: 3.635A pdb=" N THR M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 121 No H-bonds generated for 'chain 'M' and resid 119 through 121' Processing helix chain 'M' and resid 123 through 141 removed outlier: 3.651A pdb=" N GLN M 127 " --> pdb=" O ASP M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 158 Processing helix chain 'M' and resid 165 through 168 removed outlier: 4.423A pdb=" N MET M 168 " --> pdb=" O GLY M 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 165 through 168' Processing helix chain 'M' and resid 169 through 183 Processing helix chain 'M' and resid 188 through 196 removed outlier: 3.518A pdb=" N ILE M 192 " --> pdb=" O THR M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 217 Processing helix chain 'M' and resid 237 through 247 removed outlier: 4.207A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 267 removed outlier: 3.887A pdb=" N LYS M 267 " --> pdb=" O CYS M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 289 removed outlier: 3.946A pdb=" N ILE M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE M 289 " --> pdb=" O ASN M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 302 removed outlier: 4.045A pdb=" N LYS M 297 " --> pdb=" O ILE M 293 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL M 298 " --> pdb=" O THR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 319 removed outlier: 3.790A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 324 removed outlier: 3.627A pdb=" N LEU M 323 " --> pdb=" O ARG M 320 " (cutoff:3.500A) removed outlier: 4.059A 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 removed outlier: 3.621A pdb=" N GLY O 147 " --> pdb=" O ILE O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 179 Processing helix chain 'O' and resid 219 through 237 removed outlier: 3.854A 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 removed outlier: 3.525A pdb=" N ASN Q 30 " --> pdb=" O ARG Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 114 removed outlier: 3.990A pdb=" N LEU Q 111 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 346 removed outlier: 3.576A pdb=" N GLU Q 346 " --> pdb=" O LEU Q 342 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 413 Processing helix chain 'R' and resid 74 through 82 Processing helix chain 'R' and resid 234 through 244 Processing helix chain 'R' and resid 259 through 267 removed outlier: 3.855A pdb=" N GLY R 267 " --> pdb=" O MET R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 310 Processing helix chain 'R' and resid 315 through 323 removed outlier: 3.910A pdb=" N ARG R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 337 removed outlier: 3.684A pdb=" N LEU R 329 " --> pdb=" O PRO R 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 337 " --> pdb=" O LEU R 333 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 29 removed outlier: 3.882A pdb=" N SER U 7 " --> pdb=" O ASN U 3 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 47 removed outlier: 3.607A pdb=" N LEU U 35 " --> pdb=" O ASP U 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 12 removed outlier: 3.531A pdb=" N ARG V 11 " --> pdb=" O GLU V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 29 Processing helix chain 'V' and resid 35 through 55 Processing helix chain 'W' and resid 5 through 21 Processing helix chain 'W' and resid 22 through 35 removed outlier: 4.238A pdb=" N VAL W 26 " --> pdb=" O GLY W 22 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS W 35 " --> pdb=" O ALA W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 48 Processing helix chain 'W' and resid 50 through 64 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 90 through 116 removed outlier: 3.805A pdb=" N ASP W 112 " --> pdb=" O ARG W 108 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP W 114 " --> pdb=" O LYS W 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS W 115 " --> pdb=" O ASP W 111 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN W 116 " --> pdb=" O ASP W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 139 Processing helix chain 'W' and resid 161 through 163 No H-bonds generated for 'chain 'W' and resid 161 through 163' Processing helix chain 'W' and resid 164 through 190 removed outlier: 3.718A pdb=" N LYS W 168 " --> pdb=" O LYS W 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN W 169 " --> pdb=" O ASN W 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP W 170 " --> pdb=" O LYS W 166 " (cutoff:3.500A) Proline residue: W 181 - end of helix Processing helix chain 'X' and resid 124 through 139 Processing helix chain 'X' and resid 143 through 151 Processing helix chain 'X' and resid 157 through 166 Processing helix chain 'X' and resid 188 through 198 Processing helix chain 'X' and resid 207 through 214 Processing helix chain 'X' and resid 216 through 224 removed outlier: 4.410A pdb=" N THR X 220 " --> pdb=" O GLN X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 265 Processing helix chain 'X' and resid 272 through 282 removed outlier: 3.553A pdb=" N ARG X 276 " --> pdb=" O ALA X 272 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU X 281 " --> pdb=" O LYS X 277 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.728A pdb=" N VAL A 17 " --> pdb=" O ASP A1419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.663A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.704A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.595A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA7, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.586A pdb=" N HIS B1104 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.866A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.524A pdb=" N SER A 513 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 4.100A pdb=" N ILE A 566 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL H 107 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.844A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB5, first strand: chain 'A' and resid 848 through 850 removed outlier: 3.625A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN A 858 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 863 " --> pdb=" O ASN A 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1280 through 1287 removed outlier: 5.201A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP A1309 " --> pdb=" O ARG A1281 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1117 " --> pdb=" O TYR A1328 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A1328 " --> pdb=" O THR A1117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 3.885A pdb=" N ARG A1274 " --> pdb=" O THR A1141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.730A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR A1154 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU I 42 " --> pdb=" O TYR A1154 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1290 through 1292 Processing sheet with id=AC2, first strand: chain 'A' and resid 1442 through 1445 removed outlier: 3.707A pdb=" N ASP A1442 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL F 133 " --> pdb=" O MET A1444 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 109 through 111 removed outlier: 5.490A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 99 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N SER B 125 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER B 126 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG B 169 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 128 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 109 through 111 removed outlier: 4.564A pdb=" N ILE B 70 " --> pdb=" O LYS Q 333 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS Q 333 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC6, first strand: chain 'B' and resid 215 through 218 Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 227 removed outlier: 7.071A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 497 through 499 Processing sheet with id=AC9, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AD1, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.504A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.449A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 624 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.798A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.798A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 954 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 56 " --> pdb=" O VAL B 954 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.749A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.041A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.744A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD9, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AE1, first strand: chain 'B' and resid 1171 through 1174 Processing sheet with id=AE2, first strand: chain 'C' and resid 7 through 13 removed outlier: 3.723A pdb=" N GLN C 7 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 119 through 120 removed outlier: 3.722A pdb=" N VAL C 119 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 100 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 48 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.730A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE6, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.841A pdb=" N LEU D 50 " --> pdb=" O PHE G 2 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.841A pdb=" N LEU D 50 " --> pdb=" O PHE G 2 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 60 through 62 removed outlier: 4.037A pdb=" N TRP E 79 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF1, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AF2, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.098A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF4, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF5, first strand: chain 'I' and resid 83 through 86 Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.583A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.290A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 92 through 95 removed outlier: 4.752A pdb=" N ASN O 95 " --> pdb=" O ALA O 101 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA O 101 " --> pdb=" O ASN O 95 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE O 106 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL O 161 " --> pdb=" O GLN O 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE O 70 " --> pdb=" O ASN O 159 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN O 159 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA O 72 " --> pdb=" O ILE O 157 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE O 157 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL O 74 " --> pdb=" O PHE O 155 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE O 155 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE O 160 " --> pdb=" O GLY O 216 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY O 216 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU O 186 " --> pdb=" O PHE O 190 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 138 through 141 removed outlier: 4.708A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY Q 363 " --> pdb=" O TRP Q 350 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR Q 393 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU Q 118 " --> pdb=" O TYR Q 393 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE Q 395 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS Q 120 " --> pdb=" O PHE Q 395 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU R 132 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR R 217 " --> pdb=" O GLU R 132 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL R 134 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS R 211 " --> pdb=" O GLN R 138 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N PHE Q 384 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N MET Q 386 " --> pdb=" O PRO Q 102 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG Q 104 " --> pdb=" O MET Q 386 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN R 67 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASP R 60 " --> pdb=" O LYS R 211 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA R 213 " --> pdb=" O ASP R 60 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU R 62 " --> pdb=" O ALA R 213 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL R 215 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG R 66 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS R 219 " --> pdb=" O ARG R 66 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL R 68 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU R 221 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU R 70 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN R 223 " --> pdb=" O LEU R 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 313 through 314 removed outlier: 3.985A pdb=" N TRP R 313 " --> pdb=" O TYR R 349 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 243 through 254 removed outlier: 6.401A pdb=" N LEU U 243 " --> pdb=" O VAL U 267 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL U 267 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU U 245 " --> pdb=" O GLY U 265 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY U 265 " --> pdb=" O LEU U 245 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER U 261 " --> pdb=" O ASP U 249 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL U 251 " --> pdb=" O LYS U 259 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS U 259 " --> pdb=" O VAL U 251 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG U 253 " --> pdb=" O ARG U 257 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG U 257 " --> pdb=" O ARG U 253 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ARG U 257 " --> pdb=" O GLU U 284 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU U 284 " --> pdb=" O ARG U 257 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS U 259 " --> pdb=" O GLU U 282 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU U 282 " --> pdb=" O LYS U 259 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER U 261 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN U 280 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS U 263 " --> pdb=" O LYS U 278 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS U 278 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N SER V 58 " --> pdb=" O TYR U 274 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE U 276 " --> pdb=" O SER V 58 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU V 60 " --> pdb=" O PHE U 276 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS U 278 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL V 62 " --> pdb=" O LYS U 278 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN U 280 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLY V 64 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU U 282 " --> pdb=" O GLY V 64 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU V 66 " --> pdb=" O GLU U 282 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU U 284 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR V 68 " --> pdb=" O GLU U 284 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS V 59 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL V 87 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N THR V 61 " --> pdb=" O VAL V 85 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL V 85 " --> pdb=" O THR V 61 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS V 63 " --> pdb=" O CYS V 83 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS V 83 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE V 79 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR V 69 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR V 77 " --> pdb=" O TYR V 69 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE V 71 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL V 75 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP V 109 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN V 84 " --> pdb=" O SER V 107 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER V 107 " --> pdb=" O GLN V 84 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR V 86 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL V 105 " --> pdb=" O THR V 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS V 116 " --> pdb=" O CYS U 246 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 67 through 72 Processing sheet with id=AG4, first strand: chain 'W' and resid 130 through 131 removed outlier: 3.664A pdb=" N TYR W 131 " --> pdb=" O TYR W 122 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 169 through 172 removed outlier: 4.319A pdb=" N THR X 177 " --> pdb=" O ASP X 172 " (cutoff:3.500A) 1814 hydrogen bonds defined for protein. 5097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 12.34 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 43733 1.54 - 1.87: 640 1.87 - 2.20: 0 2.20 - 2.53: 0 2.53 - 2.86: 1 Bond restraints: 44374 Sorted by residual: bond pdb=" C LEU X 181 " pdb=" N THR X 183 " ideal model delta sigma weight residual 1.332 2.864 -1.531 1.40e-02 5.10e+03 1.20e+04 bond pdb=" C THR B1213 " pdb=" N PRO B1214 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.44e+01 bond pdb=" C THR Q 403 " pdb=" N LEU Q 404 " ideal model delta sigma weight residual 1.332 1.368 -0.035 1.40e-02 5.10e+03 6.42e+00 bond pdb=" C LEU Q 404 " pdb=" N THR Q 405 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.40e-02 5.10e+03 4.79e+00 bond pdb=" C ALA A1434 " pdb=" N PRO A1435 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.53e+00 ... (remaining 44369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 60341 4.59 - 9.18: 32 9.18 - 13.77: 1 13.77 - 18.36: 0 18.36 - 22.94: 1 Bond angle restraints: 60375 Sorted by residual: angle pdb=" O LEU X 181 " pdb=" C LEU X 181 " pdb=" N THR X 183 " ideal model delta sigma weight residual 122.59 99.65 22.94 1.33e+00 5.65e-01 2.98e+02 angle pdb=" C ILE E 127 " pdb=" N PRO E 128 " pdb=" CA PRO E 128 " ideal model delta sigma weight residual 119.66 124.37 -4.71 7.20e-01 1.93e+00 4.29e+01 angle pdb=" C VAL A1146 " pdb=" N THR A1147 " pdb=" CA THR A1147 " ideal model delta sigma weight residual 122.77 114.35 8.42 1.33e+00 5.65e-01 4.01e+01 angle pdb=" N CYS I 29 " pdb=" CA CYS I 29 " pdb=" C CYS I 29 " ideal model delta sigma weight residual 108.34 100.58 7.76 1.64e+00 3.72e-01 2.24e+01 angle pdb=" O PRO E 128 " pdb=" C PRO E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 121.15 123.12 -1.97 4.70e-01 4.53e+00 1.75e+01 ... (remaining 60370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 25360 17.83 - 35.67: 938 35.67 - 53.50: 438 53.50 - 71.34: 83 71.34 - 89.17: 20 Dihedral angle restraints: 26839 sinusoidal: 11574 harmonic: 15265 Sorted by residual: dihedral pdb=" CA LEU X 181 " pdb=" C LEU X 181 " pdb=" N THR X 183 " pdb=" CA THR X 183 " ideal model delta harmonic sigma weight residual 180.00 -96.10 -83.90 0 5.00e+00 4.00e-02 2.82e+02 dihedral pdb=" CA LYS Q 333 " pdb=" C LYS Q 333 " pdb=" N VAL Q 334 " pdb=" CA VAL Q 334 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ASP O 81 " pdb=" C ASP O 81 " pdb=" N LEU O 82 " pdb=" CA LEU O 82 " ideal model delta harmonic sigma weight residual -180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 26836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5798 0.050 - 0.101: 813 0.101 - 0.151: 238 0.151 - 0.202: 3 0.202 - 0.252: 4 Chirality restraints: 6856 Sorted by residual: chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA CYS I 29 " pdb=" N CYS I 29 " pdb=" C CYS I 29 " pdb=" CB CYS I 29 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PRO W 77 " pdb=" N PRO W 77 " pdb=" C PRO W 77 " pdb=" CB PRO W 77 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 6853 not shown) Planarity restraints: 7399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU X 181 " 0.125 2.00e-02 2.50e+03 1.84e-01 3.37e+02 pdb=" C LEU X 181 " -0.312 2.00e-02 2.50e+03 pdb=" O LEU X 181 " 0.140 2.00e-02 2.50e+03 pdb=" N THR X 183 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 73 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.10e+00 pdb=" N PRO R 74 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 74 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 74 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 333 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C LYS Q 333 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS Q 333 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL Q 334 " -0.015 2.00e-02 2.50e+03 ... (remaining 7396 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.67: 11 1.67 - 2.48: 231 2.48 - 3.28: 46043 3.28 - 4.09: 105489 4.09 - 4.90: 191496 Warning: very small nonbonded interaction distances. Nonbonded interactions: 343270 Sorted by model distance: nonbonded pdb=" C LYS M 272 " pdb=" OP1 DG T 66 " model vdw 0.860 3.270 nonbonded pdb=" OP1 DG T 41 " pdb=" CB SER W 81 " model vdw 1.064 3.440 nonbonded pdb=" CA LYS M 272 " pdb=" OP1 DG T 66 " model vdw 1.078 3.470 nonbonded pdb=" NE ARG O 98 " pdb=" OP1 DA T 58 " model vdw 1.217 3.120 nonbonded pdb=" CB LYS M 272 " pdb=" P DG T 66 " model vdw 1.365 3.800 ... (remaining 343265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 1.860 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: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 47.790 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0004 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 : 0.008 1.531 44414 Z= 0.537 Angle : 0.696 36.359 60432 Z= 0.299 Chirality : 0.039 0.252 6856 Planarity : 0.004 0.184 7399 Dihedral : 11.781 89.170 16925 Min Nonbonded Distance : 0.860 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.21 % Favored : 92.76 % Rotamer: Outliers : 0.16 % Allowed : 4.26 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.33 (0.10), residues: 5154 helix: -2.28 (0.09), residues: 1947 sheet: -1.62 (0.16), residues: 931 loop : -2.26 (0.11), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1055 TYR 0.012 0.001 TYR Q 401 PHE 0.014 0.001 PHE B 429 TRP 0.008 0.001 TRP R 81 HIS 0.014 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00759 (44374) covalent geometry : angle 0.47354 (60375) hydrogen bonds : bond 0.13538 ( 1905) hydrogen bonds : angle 8.89037 ( 5345) metal coordination : bond 0.08184 ( 40) metal coordination : angle 16.63274 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 676 time to evaluate : 1.679 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 376 TYR cc_start: -0.1622 (t80) cc_final: -0.3566 (t80) REVERT: A 455 MET cc_start: 0.1715 (mtp) cc_final: 0.1466 (mtp) REVERT: A 849 MET cc_start: 0.3756 (pmm) cc_final: 0.2258 (ttm) REVERT: A 1063 MET cc_start: -0.1124 (mmm) cc_final: -0.1500 (mmm) REVERT: A 1259 MET cc_start: -0.1459 (tmt) cc_final: -0.3695 (ptt) REVERT: A 1327 ILE cc_start: 0.4737 (tt) cc_final: 0.4138 (tt) REVERT: A 1378 GLN cc_start: 0.5843 (mm-40) cc_final: 0.3449 (mp10) REVERT: B 199 MET cc_start: -0.2562 (ptp) cc_final: -0.3585 (ptp) REVERT: B 463 THR cc_start: 0.4008 (p) cc_final: 0.3400 (t) REVERT: B 542 MET cc_start: 0.3876 (mtp) cc_final: 0.3644 (ptt) REVERT: B 970 THR cc_start: 0.4230 (m) cc_final: 0.3692 (m) REVERT: B 1025 HIS cc_start: 0.1638 (t-90) cc_final: 0.1220 (t-90) REVERT: B 1092 TYR cc_start: 0.1278 (m-80) cc_final: 0.0494 (m-80) REVERT: B 1110 PRO cc_start: -0.1134 (Cg_endo) cc_final: -0.1362 (Cg_exo) REVERT: B 1210 MET cc_start: 0.2845 (ttt) cc_final: 0.1687 (ptm) REVERT: C 75 MET cc_start: -0.3509 (tpp) cc_final: -0.4674 (mmt) REVERT: C 222 LYS cc_start: 0.2129 (pmtt) cc_final: 0.1602 (mmtt) REVERT: F 88 TYR cc_start: 0.2603 (m-80) cc_final: -0.0839 (m-80) REVERT: G 12 THR cc_start: -0.0882 (m) cc_final: -0.1118 (p) REVERT: Q 27 MET cc_start: 0.2198 (mmm) cc_final: 0.0470 (tpt) REVERT: U 258 TRP cc_start: -0.0007 (m100) cc_final: -0.0581 (m100) REVERT: V 51 THR cc_start: 0.7687 (m) cc_final: 0.7252 (t) REVERT: W 30 ASP cc_start: 0.5146 (m-30) cc_final: 0.4808 (m-30) outliers start: 7 outliers final: 3 residues processed: 681 average time/residue: 0.2873 time to fit residues: 308.1633 Evaluate side-chains 381 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 378 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 30.0000 chunk 366 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 45 GLN A 64 ASN A 68 GLN A 75 ASN A 213 HIS A 311 GLN A 313 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 399 HIS A 435 HIS ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A 525 GLN A 548 ASN A 640 GLN A 660 ASN A 698 GLN A 717 ASN A 723 ASN A 741 ASN A 745 GLN A 760 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 968 GLN A 994 GLN A1040 GLN A1130 GLN A1378 GLN B 60 GLN B 395 GLN B 415 GLN B 433 GLN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN B 518 HIS B 538 ASN B 573 GLN ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN B1093 GLN B1112 GLN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 224 GLN C 242 GLN C 264 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN E 54 GLN E 146 HIS G 102 GLN G 158 HIS H 83 GLN H 133 ASN I 12 ASN K 2 ASN K 112 GLN M 90 ASN M 124 ASN M 208 ASN O 91 ASN O 179 HIS Q 117 HIS U 33 GLN U 280 GLN V 84 GLN W 138 GLN X 216 GLN X 267 GLN X 279 GLN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.157759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.132068 restraints weight = 115839.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.132761 restraints weight = 84506.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.133892 restraints weight = 63961.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.134243 restraints weight = 52176.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.134693 restraints weight = 49892.426| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1040 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 44414 Z= 0.236 Angle : 0.829 16.466 60432 Z= 0.416 Chirality : 0.047 0.297 6856 Planarity : 0.007 0.103 7399 Dihedral : 13.736 82.718 6846 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.11 % Favored : 95.54 % Rotamer: Outliers : 0.27 % Allowed : 3.38 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.11), residues: 5156 helix: -0.73 (0.11), residues: 1981 sheet: -1.14 (0.16), residues: 880 loop : -1.94 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B1094 TYR 0.032 0.003 TYR Q 393 PHE 0.057 0.003 PHE A 81 TRP 0.024 0.003 TRP B 681 HIS 0.016 0.002 HIS B1141 Details of bonding type rmsd covalent geometry : bond 0.00520 (44374) covalent geometry : angle 0.79280 (60375) hydrogen bonds : bond 0.04727 ( 1905) hydrogen bonds : angle 5.92137 ( 5345) metal coordination : bond 0.01818 ( 40) metal coordination : angle 7.88530 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 485 time to evaluate : 1.418 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: A 41 MET cc_start: -0.1456 (mmp) cc_final: -0.2062 (mmm) REVERT: A 199 LEU cc_start: 0.5724 (mp) cc_final: 0.5355 (tp) REVERT: A 376 TYR cc_start: 0.0134 (t80) cc_final: -0.2756 (p90) REVERT: A 434 ARG cc_start: 0.4520 (ttt90) cc_final: 0.3927 (mtp180) REVERT: A 456 MET cc_start: -0.0878 (ttm) cc_final: -0.1105 (ttm) REVERT: A 468 PHE cc_start: 0.0026 (OUTLIER) cc_final: -0.2241 (m-10) REVERT: A 849 MET cc_start: 0.5133 (pmm) cc_final: 0.2411 (ttp) REVERT: A 1063 MET cc_start: -0.0631 (mmm) cc_final: -0.0939 (mmm) REVERT: A 1167 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 199 MET cc_start: -0.1795 (ptp) cc_final: -0.2564 (ptp) REVERT: B 296 GLU cc_start: 0.2844 (tt0) cc_final: 0.2623 (mp0) REVERT: B 542 MET cc_start: 0.4440 (mtp) cc_final: 0.3848 (ptt) REVERT: B 618 ASP cc_start: 0.7602 (p0) cc_final: 0.7391 (p0) REVERT: B 778 MET cc_start: 0.2403 (mtt) cc_final: 0.0820 (ptp) REVERT: B 910 VAL cc_start: 0.6018 (t) cc_final: 0.5765 (t) REVERT: B 935 ARG cc_start: 0.5373 (ttp-110) cc_final: 0.4561 (ttt90) REVERT: B 980 PHE cc_start: 0.1121 (m-80) cc_final: -0.0114 (m-80) REVERT: B 1110 PRO cc_start: 0.1043 (Cg_endo) cc_final: 0.0137 (Cg_exo) REVERT: B 1112 GLN cc_start: 0.4128 (OUTLIER) cc_final: 0.3801 (pt0) REVERT: B 1165 ILE cc_start: 0.2473 (tt) cc_final: 0.2201 (tt) REVERT: B 1201 LYS cc_start: 0.5350 (tttp) cc_final: 0.5105 (tttp) REVERT: C 222 LYS cc_start: 0.2692 (pttm) cc_final: 0.2290 (mptt) REVERT: E 148 GLU cc_start: 0.4791 (pm20) cc_final: 0.4206 (pp20) REVERT: E 215 MET cc_start: 0.3765 (mtt) cc_final: 0.3455 (mtt) REVERT: F 88 TYR cc_start: 0.2120 (m-80) cc_final: 0.0888 (m-10) REVERT: I 86 PHE cc_start: 0.6034 (p90) cc_final: 0.5793 (p90) REVERT: J 63 TYR cc_start: 0.3051 (m-80) cc_final: 0.1125 (m-80) REVERT: M 172 MET cc_start: 0.3092 (tmm) cc_final: 0.2746 (tmm) REVERT: M 192 ILE cc_start: 0.8078 (tt) cc_final: 0.7270 (tt) REVERT: O 114 LEU cc_start: 0.7759 (mt) cc_final: 0.7227 (mp) REVERT: O 219 GLN cc_start: 0.7165 (pt0) cc_final: 0.6957 (pt0) REVERT: R 75 MET cc_start: 0.5815 (ppp) cc_final: 0.4257 (tpt) REVERT: U 258 TRP cc_start: 0.0115 (m100) cc_final: -0.0186 (m100) REVERT: V 51 THR cc_start: 0.9075 (m) cc_final: 0.8407 (p) REVERT: W 30 ASP cc_start: 0.5980 (m-30) cc_final: 0.5444 (p0) REVERT: W 169 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8418 (tp-100) REVERT: W 172 LEU cc_start: 0.8573 (mt) cc_final: 0.8272 (mt) outliers start: 12 outliers final: 0 residues processed: 495 average time/residue: 0.2778 time to fit residues: 222.0650 Evaluate side-chains 364 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 362 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 62 optimal weight: 0.7980 chunk 340 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 290 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 429 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 299 HIS A 316 GLN ** A 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 576 GLN A 717 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS B 518 HIS B 822 ASN B 862 GLN ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS I 60 GLN M 158 HIS ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.158133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.131881 restraints weight = 118763.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133200 restraints weight = 88878.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.133655 restraints weight = 69129.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.134332 restraints weight = 58106.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.134642 restraints weight = 51975.368| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1079 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 44414 Z= 0.151 Angle : 0.648 13.879 60432 Z= 0.323 Chirality : 0.043 0.273 6856 Planarity : 0.005 0.091 7399 Dihedral : 13.694 78.456 6846 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.60 % Favored : 95.07 % Rotamer: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.11), residues: 5156 helix: -0.07 (0.11), residues: 1974 sheet: -0.85 (0.17), residues: 851 loop : -1.82 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 28 TYR 0.023 0.002 TYR Q 393 PHE 0.019 0.002 PHE A 813 TRP 0.025 0.001 TRP X 263 HIS 0.011 0.001 HIS B1141 Details of bonding type rmsd covalent geometry : bond 0.00329 (44374) covalent geometry : angle 0.61687 (60375) hydrogen bonds : bond 0.03735 ( 1905) hydrogen bonds : angle 5.36169 ( 5345) metal coordination : bond 0.01628 ( 40) metal coordination : angle 6.43732 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 424 time to evaluate : 1.645 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: A 199 LEU cc_start: 0.5731 (mp) cc_final: 0.5425 (pt) REVERT: A 341 MET cc_start: -0.0745 (tpp) cc_final: -0.1539 (tpp) REVERT: A 376 TYR cc_start: -0.0374 (t80) cc_final: -0.3230 (p90) REVERT: A 456 MET cc_start: 0.0144 (ttm) cc_final: -0.0415 (ttm) REVERT: A 849 MET cc_start: 0.5013 (pmm) cc_final: 0.2679 (ttt) REVERT: A 1063 MET cc_start: -0.0181 (mmm) cc_final: -0.0858 (mmm) REVERT: A 1167 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 199 MET cc_start: -0.1896 (ptp) cc_final: -0.3092 (pmm) REVERT: B 542 MET cc_start: 0.4713 (mtp) cc_final: 0.4127 (ttp) REVERT: B 618 ASP cc_start: 0.7065 (p0) cc_final: 0.6513 (p0) REVERT: B 778 MET cc_start: 0.1247 (mtt) cc_final: 0.0729 (mtm) REVERT: B 910 VAL cc_start: 0.5591 (t) cc_final: 0.5342 (t) REVERT: B 935 ARG cc_start: 0.5369 (ttp-110) cc_final: 0.4516 (ttt90) REVERT: B 967 ARG cc_start: 0.5065 (tpp80) cc_final: 0.4814 (tpt-90) REVERT: B 980 PHE cc_start: 0.0809 (m-80) cc_final: -0.0967 (m-80) REVERT: B 1072 MET cc_start: -0.1416 (mmt) cc_final: -0.1659 (mmt) REVERT: B 1110 PRO cc_start: -0.0260 (Cg_endo) cc_final: -0.0607 (Cg_exo) REVERT: B 1169 MET cc_start: 0.3749 (tmm) cc_final: 0.1711 (tpt) REVERT: B 1174 LYS cc_start: 0.6720 (ptpp) cc_final: 0.6259 (tppt) REVERT: C 81 GLU cc_start: 0.5911 (pt0) cc_final: 0.5478 (pm20) REVERT: D 145 MET cc_start: -0.4714 (mmp) cc_final: -0.4975 (mmt) REVERT: D 176 GLU cc_start: 0.6564 (tt0) cc_final: 0.5953 (tp30) REVERT: E 22 MET cc_start: 0.2374 (tpt) cc_final: -0.1009 (mtt) REVERT: E 148 GLU cc_start: 0.4576 (pm20) cc_final: 0.4080 (pp20) REVERT: E 215 MET cc_start: 0.3356 (mtt) cc_final: 0.3072 (mtt) REVERT: F 88 TYR cc_start: 0.2055 (m-80) cc_final: 0.0564 (m-10) REVERT: H 7 ASP cc_start: 0.4382 (p0) cc_final: 0.4165 (p0) REVERT: I 13 MET cc_start: 0.6029 (ppp) cc_final: 0.5813 (ppp) REVERT: M 172 MET cc_start: 0.2816 (tmm) cc_final: 0.2558 (tmm) REVERT: M 210 MET cc_start: 0.0432 (ptp) cc_final: -0.0061 (tpt) REVERT: O 114 LEU cc_start: 0.7485 (mt) cc_final: 0.6978 (mp) REVERT: O 121 MET cc_start: 0.8448 (ptp) cc_final: 0.8058 (mpp) REVERT: Q 27 MET cc_start: 0.2829 (mmp) cc_final: 0.0191 (tpt) REVERT: U 258 TRP cc_start: 0.0203 (m100) cc_final: -0.0681 (m100) REVERT: V 81 LYS cc_start: 0.7462 (mmtp) cc_final: 0.7132 (tmtt) REVERT: W 169 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8614 (tp-100) REVERT: W 172 LEU cc_start: 0.8598 (mt) cc_final: 0.8278 (mt) REVERT: X 263 TRP cc_start: 0.5606 (t-100) cc_final: 0.5247 (t-100) outliers start: 3 outliers final: 0 residues processed: 426 average time/residue: 0.2661 time to fit residues: 184.0233 Evaluate side-chains 352 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 383 optimal weight: 6.9990 chunk 438 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 420 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 410 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 257 optimal weight: 0.7980 chunk 367 optimal weight: 5.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A 768 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN A1048 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN D 37 GLN E 146 HIS ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS O 159 ASN O 219 GLN ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 138 GLN ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.165155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.145670 restraints weight = 140991.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.145205 restraints weight = 162964.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.146760 restraints weight = 135610.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.146790 restraints weight = 106480.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.147161 restraints weight = 90119.993| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1361 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 44414 Z= 0.198 Angle : 0.787 35.779 60432 Z= 0.385 Chirality : 0.046 0.375 6856 Planarity : 0.006 0.088 7399 Dihedral : 13.924 80.797 6846 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.18 % Favored : 94.55 % Rotamer: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.11), residues: 5156 helix: -0.06 (0.11), residues: 1971 sheet: -0.78 (0.17), residues: 836 loop : -1.93 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1067 TYR 0.027 0.002 TYR B 380 PHE 0.034 0.003 PHE A 468 TRP 0.016 0.002 TRP X 263 HIS 0.011 0.002 HIS B1141 Details of bonding type rmsd covalent geometry : bond 0.00435 (44374) covalent geometry : angle 0.74178 (60375) hydrogen bonds : bond 0.04241 ( 1905) hydrogen bonds : angle 5.42600 ( 5345) metal coordination : bond 0.01371 ( 40) metal coordination : angle 8.63767 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 426 time to evaluate : 1.539 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: A 341 MET cc_start: -0.0316 (tpp) cc_final: -0.0863 (tpp) REVERT: A 376 TYR cc_start: 0.0050 (t80) cc_final: -0.3305 (p90) REVERT: A 394 ASN cc_start: 0.6509 (m-40) cc_final: 0.5978 (p0) REVERT: A 433 GLU cc_start: 0.4980 (mp0) cc_final: 0.4564 (mp0) REVERT: A 676 MET cc_start: -0.1572 (tmm) cc_final: -0.2179 (tmm) REVERT: A 900 ASP cc_start: 0.2460 (m-30) cc_final: 0.2238 (m-30) REVERT: A 1063 MET cc_start: 0.1108 (mmm) cc_final: 0.0660 (tpp) REVERT: A 1111 MET cc_start: -0.1494 (mmt) cc_final: -0.1942 (mmt) REVERT: B 199 MET cc_start: -0.1637 (ptp) cc_final: -0.2891 (pmm) REVERT: B 444 MET cc_start: 0.1081 (ptt) cc_final: 0.0837 (ptp) REVERT: B 542 MET cc_start: 0.5484 (mtp) cc_final: 0.4484 (ttp) REVERT: B 778 MET cc_start: 0.1304 (mtt) cc_final: 0.0867 (mtp) REVERT: B 935 ARG cc_start: 0.5339 (ttp-110) cc_final: 0.4389 (ttt90) REVERT: B 1072 MET cc_start: -0.0769 (mmt) cc_final: -0.1519 (mmt) REVERT: B 1110 PRO cc_start: 0.0673 (Cg_endo) cc_final: -0.1204 (Cg_exo) REVERT: B 1169 MET cc_start: 0.3468 (tmm) cc_final: 0.2988 (tmm) REVERT: B 1174 LYS cc_start: 0.7254 (ptpp) cc_final: 0.6751 (tppt) REVERT: B 1201 LYS cc_start: 0.4718 (tttp) cc_final: 0.4398 (tttt) REVERT: C 81 GLU cc_start: 0.5941 (pt0) cc_final: 0.5263 (pm20) REVERT: D 145 MET cc_start: -0.4530 (mmp) cc_final: -0.4996 (mmt) REVERT: D 176 GLU cc_start: 0.6389 (tt0) cc_final: 0.5584 (tp30) REVERT: E 197 LYS cc_start: 0.6509 (tptp) cc_final: 0.6012 (tptt) REVERT: E 215 MET cc_start: 0.3587 (mtt) cc_final: 0.3299 (mtt) REVERT: F 88 TYR cc_start: 0.1843 (m-80) cc_final: 0.0591 (m-10) REVERT: H 7 ASP cc_start: 0.4666 (p0) cc_final: 0.4245 (p0) REVERT: M 210 MET cc_start: 0.0929 (ptp) cc_final: 0.0026 (tpt) REVERT: O 114 LEU cc_start: 0.6750 (mt) cc_final: 0.6095 (mp) REVERT: U 278 LYS cc_start: 0.6483 (mtmm) cc_final: 0.6073 (pttt) REVERT: V 50 GLU cc_start: 0.9202 (pp20) cc_final: 0.8996 (pp20) REVERT: V 51 THR cc_start: 0.8162 (p) cc_final: 0.7959 (p) REVERT: V 81 LYS cc_start: 0.7579 (mmtp) cc_final: 0.7179 (tmtt) REVERT: V 116 CYS cc_start: 0.7725 (m) cc_final: 0.7524 (t) REVERT: W 30 ASP cc_start: 0.6917 (p0) cc_final: 0.5488 (m-30) REVERT: W 169 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8527 (tp-100) REVERT: W 172 LEU cc_start: 0.8401 (mt) cc_final: 0.8116 (mt) outliers start: 4 outliers final: 2 residues processed: 429 average time/residue: 0.2542 time to fit residues: 177.9382 Evaluate side-chains 354 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 352 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 331 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 464 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 332 optimal weight: 0.0980 chunk 242 optimal weight: 6.9990 chunk 465 optimal weight: 8.9990 chunk 335 optimal weight: 30.0000 chunk 190 optimal weight: 2.9990 chunk 481 optimal weight: 40.0000 chunk 197 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS A 700 ASN A 717 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN A1048 ASN A1312 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 HIS B 415 GLN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS B1195 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.159912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.134430 restraints weight = 120181.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.135934 restraints weight = 85894.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.137220 restraints weight = 63289.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137914 restraints weight = 48244.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.138190 restraints weight = 46784.319| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1335 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44414 Z= 0.136 Angle : 0.659 28.262 60432 Z= 0.322 Chirality : 0.043 0.225 6856 Planarity : 0.005 0.097 7399 Dihedral : 13.914 78.946 6846 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.91 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.11), residues: 5156 helix: 0.31 (0.12), residues: 1967 sheet: -0.65 (0.18), residues: 794 loop : -1.80 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1106 TYR 0.017 0.001 TYR B1092 PHE 0.041 0.002 PHE A 468 TRP 0.037 0.001 TRP X 263 HIS 0.011 0.001 HIS B1141 Details of bonding type rmsd covalent geometry : bond 0.00298 (44374) covalent geometry : angle 0.61338 (60375) hydrogen bonds : bond 0.03581 ( 1905) hydrogen bonds : angle 5.10272 ( 5345) metal coordination : bond 0.01273 ( 40) metal coordination : angle 7.83905 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.507 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: A 6 TYR cc_start: 0.2406 (p90) cc_final: 0.1343 (m-80) REVERT: A 341 MET cc_start: -0.0744 (tpp) cc_final: -0.1211 (tpp) REVERT: A 376 TYR cc_start: -0.0063 (t80) cc_final: -0.3304 (p90) REVERT: A 433 GLU cc_start: 0.5122 (mp0) cc_final: 0.4569 (mp0) REVERT: A 849 MET cc_start: 0.5472 (pmm) cc_final: 0.3232 (ptm) REVERT: A 1063 MET cc_start: 0.1133 (mmm) cc_final: 0.0267 (tpp) REVERT: B 199 MET cc_start: -0.1990 (ptp) cc_final: -0.3032 (pmm) REVERT: B 444 MET cc_start: 0.0750 (ptt) cc_final: 0.0527 (ptp) REVERT: B 542 MET cc_start: 0.5424 (mtp) cc_final: 0.4865 (ttm) REVERT: B 778 MET cc_start: 0.0481 (mtt) cc_final: 0.0189 (mtm) REVERT: B 935 ARG cc_start: 0.5512 (ttp-110) cc_final: 0.4361 (ttt90) REVERT: B 1072 MET cc_start: -0.0729 (mmt) cc_final: -0.1184 (mmt) REVERT: B 1120 GLU cc_start: 0.1627 (tp30) cc_final: 0.0628 (tt0) REVERT: B 1169 MET cc_start: 0.2652 (tmm) cc_final: 0.2142 (tmm) REVERT: B 1174 LYS cc_start: 0.7281 (ptpp) cc_final: 0.6831 (tppt) REVERT: D 176 GLU cc_start: 0.6632 (tt0) cc_final: 0.5828 (tp30) REVERT: E 22 MET cc_start: 0.3147 (tpt) cc_final: 0.0014 (mtt) REVERT: E 197 LYS cc_start: 0.6525 (tptp) cc_final: 0.6065 (tptt) REVERT: E 215 MET cc_start: 0.3460 (mtt) cc_final: 0.3067 (mtt) REVERT: F 88 TYR cc_start: 0.1612 (m-80) cc_final: 0.0536 (m-80) REVERT: H 7 ASP cc_start: 0.4388 (p0) cc_final: 0.4147 (p0) REVERT: I 13 MET cc_start: 0.6072 (ppp) cc_final: 0.5658 (ppp) REVERT: J 57 ILE cc_start: 0.2234 (tt) cc_final: 0.1768 (mt) REVERT: O 114 LEU cc_start: 0.7338 (mt) cc_final: 0.6829 (mp) REVERT: V 51 THR cc_start: 0.8411 (p) cc_final: 0.8157 (p) REVERT: V 81 LYS cc_start: 0.7549 (mmtp) cc_final: 0.7228 (tmtt) REVERT: W 30 ASP cc_start: 0.7248 (p0) cc_final: 0.6064 (m-30) REVERT: W 169 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8818 (tp-100) REVERT: W 172 LEU cc_start: 0.8662 (mt) cc_final: 0.8278 (mt) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2673 time to fit residues: 173.9431 Evaluate side-chains 343 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 96 optimal weight: 8.9990 chunk 351 optimal weight: 3.9990 chunk 428 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 345 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A 881 GLN A1059 HIS ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 443 ASN ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 GLN B 770 GLN B1097 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN M 124 ASN Q 117 HIS ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.161934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.137562 restraints weight = 120183.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.140345 restraints weight = 80489.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.141472 restraints weight = 54868.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.142722 restraints weight = 41971.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.143432 restraints weight = 33799.628| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1690 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 44414 Z= 0.229 Angle : 0.868 39.517 60432 Z= 0.428 Chirality : 0.048 0.296 6856 Planarity : 0.007 0.154 7399 Dihedral : 14.265 80.576 6846 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.28 % Favored : 93.41 % Rotamer: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.11), residues: 5156 helix: 0.05 (0.12), residues: 1960 sheet: -0.84 (0.18), residues: 771 loop : -1.99 (0.11), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1001 TYR 0.035 0.003 TYR A 6 PHE 0.045 0.003 PHE B 980 TRP 0.100 0.003 TRP U 258 HIS 0.030 0.002 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00510 (44374) covalent geometry : angle 0.82366 (60375) hydrogen bonds : bond 0.04765 ( 1905) hydrogen bonds : angle 5.62180 ( 5345) metal coordination : bond 0.01144 ( 40) metal coordination : angle 9.00549 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 1.510 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: A 6 TYR cc_start: 0.3589 (p90) cc_final: 0.2867 (m-80) REVERT: A 7 SER cc_start: 0.5128 (t) cc_final: 0.4583 (t) REVERT: A 146 MET cc_start: -0.1227 (mmp) cc_final: -0.1859 (mmp) REVERT: A 341 MET cc_start: -0.0266 (tpp) cc_final: -0.0942 (tpp) REVERT: A 394 ASN cc_start: 0.6182 (m-40) cc_final: 0.5692 (p0) REVERT: A 433 GLU cc_start: 0.5283 (mp0) cc_final: 0.4839 (mp0) REVERT: A 748 MET cc_start: 0.0234 (ptt) cc_final: -0.0431 (tmm) REVERT: A 849 MET cc_start: 0.5971 (pmm) cc_final: 0.2814 (ttp) REVERT: A 1063 MET cc_start: 0.1903 (mmm) cc_final: 0.1296 (tpp) REVERT: A 1111 MET cc_start: -0.0696 (mmt) cc_final: -0.1193 (mmt) REVERT: A 1433 MET cc_start: 0.2776 (tpp) cc_final: 0.1791 (ppp) REVERT: B 199 MET cc_start: -0.1109 (ptp) cc_final: -0.1368 (ptp) REVERT: B 310 MET cc_start: -0.5645 (mtm) cc_final: -0.6049 (mtm) REVERT: B 542 MET cc_start: 0.5365 (mtp) cc_final: 0.4945 (ttt) REVERT: B 597 MET cc_start: 0.7082 (ttm) cc_final: 0.6743 (ttp) REVERT: B 601 ARG cc_start: 0.4523 (mmt180) cc_final: 0.3656 (mmt180) REVERT: B 778 MET cc_start: 0.1406 (mtt) cc_final: 0.0628 (mtm) REVERT: B 1064 TYR cc_start: 0.4872 (m-10) cc_final: 0.4189 (m-10) REVERT: B 1072 MET cc_start: -0.0400 (mmt) cc_final: -0.1182 (mmt) REVERT: D 176 GLU cc_start: 0.6786 (tt0) cc_final: 0.5957 (tp30) REVERT: E 197 LYS cc_start: 0.6714 (tptp) cc_final: 0.6245 (tptt) REVERT: E 215 MET cc_start: 0.3925 (mtt) cc_final: 0.3423 (mtt) REVERT: F 88 TYR cc_start: 0.1512 (m-80) cc_final: 0.0706 (m-80) REVERT: H 7 ASP cc_start: 0.4834 (p0) cc_final: 0.4623 (p0) REVERT: M 217 LYS cc_start: 0.5971 (mmmt) cc_final: 0.5088 (pptt) REVERT: Q 101 PHE cc_start: 0.8230 (m-80) cc_final: 0.7982 (m-80) REVERT: V 81 LYS cc_start: 0.7648 (mmtp) cc_final: 0.7422 (pptt) REVERT: W 122 TYR cc_start: 0.5291 (m-10) cc_final: 0.5058 (m-80) REVERT: W 169 GLN cc_start: 0.9283 (tp-100) cc_final: 0.8927 (tp-100) REVERT: W 172 LEU cc_start: 0.8836 (mt) cc_final: 0.8457 (mt) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.2739 time to fit residues: 184.6899 Evaluate side-chains 335 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 303 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 473 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 418 optimal weight: 9.9990 chunk 347 optimal weight: 0.0470 chunk 441 optimal weight: 40.0000 chunk 450 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A 736 ASN A 768 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 400 HIS B 516 ASN B 538 ASN B 951 GLN B1040 ASN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS E 8 ASN G 71 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 HIS U 280 GLN W 133 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.163643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.140088 restraints weight = 120630.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.143164 restraints weight = 80058.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.144502 restraints weight = 52657.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.145084 restraints weight = 41853.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.145936 restraints weight = 36259.783| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1769 moved from start: 0.7710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 44414 Z= 0.211 Angle : 0.849 44.153 60432 Z= 0.417 Chirality : 0.048 0.319 6856 Planarity : 0.007 0.126 7399 Dihedral : 14.475 77.585 6846 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.46 % Favored : 93.27 % Rotamer: Outliers : 0.02 % Allowed : 1.73 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.11), residues: 5156 helix: -0.04 (0.12), residues: 1955 sheet: -0.97 (0.18), residues: 787 loop : -2.01 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 728 TYR 0.044 0.002 TYR C 180 PHE 0.059 0.003 PHE A 468 TRP 0.051 0.003 TRP A 572 HIS 0.015 0.002 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.00466 (44374) covalent geometry : angle 0.79866 (60375) hydrogen bonds : bond 0.04558 ( 1905) hydrogen bonds : angle 5.70969 ( 5345) metal coordination : bond 0.01796 ( 40) metal coordination : angle 9.37231 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 406 time to evaluate : 1.549 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: A 6 TYR cc_start: 0.4124 (p90) cc_final: 0.2854 (m-80) REVERT: A 95 PHE cc_start: 0.5998 (m-10) cc_final: 0.5575 (m-10) REVERT: A 146 MET cc_start: -0.1199 (mmp) cc_final: -0.1823 (mmp) REVERT: A 341 MET cc_start: -0.0073 (tpp) cc_final: -0.1030 (tpp) REVERT: A 433 GLU cc_start: 0.5489 (mp0) cc_final: 0.5215 (mp0) REVERT: A 685 GLU cc_start: 0.8414 (tt0) cc_final: 0.7348 (tm-30) REVERT: A 748 MET cc_start: 0.0582 (ptt) cc_final: -0.0857 (tmm) REVERT: A 849 MET cc_start: 0.6051 (pmm) cc_final: 0.3194 (ttp) REVERT: A 1063 MET cc_start: 0.1909 (mmm) cc_final: 0.1565 (tpp) REVERT: A 1187 GLN cc_start: 0.6609 (tm-30) cc_final: 0.6357 (tm-30) REVERT: A 1433 MET cc_start: 0.3139 (tpp) cc_final: 0.2201 (ppp) REVERT: B 310 MET cc_start: -0.5772 (mtm) cc_final: -0.6324 (mpp) REVERT: B 542 MET cc_start: 0.5314 (mtp) cc_final: 0.4431 (ttp) REVERT: B 601 ARG cc_start: 0.4887 (mmt180) cc_final: 0.4224 (mmt180) REVERT: B 789 MET cc_start: 0.5985 (tpp) cc_final: 0.5719 (tpp) REVERT: B 1072 MET cc_start: -0.0458 (mmt) cc_final: -0.0695 (mmt) REVERT: D 176 GLU cc_start: 0.6754 (tt0) cc_final: 0.5951 (tp30) REVERT: E 22 MET cc_start: 0.3552 (tpt) cc_final: 0.0909 (mtt) REVERT: E 197 LYS cc_start: 0.6762 (tptp) cc_final: 0.6393 (tptt) REVERT: E 215 MET cc_start: 0.4582 (mtt) cc_final: 0.4001 (mtt) REVERT: F 88 TYR cc_start: 0.1351 (m-80) cc_final: 0.0898 (m-80) REVERT: G 37 SER cc_start: 0.6311 (m) cc_final: 0.5859 (m) REVERT: I 13 MET cc_start: 0.5436 (ppp) cc_final: 0.5096 (ppp) REVERT: I 86 PHE cc_start: 0.6761 (p90) cc_final: 0.6479 (p90) REVERT: L 58 LYS cc_start: 0.5450 (tptt) cc_final: 0.4773 (tptt) REVERT: Q 101 PHE cc_start: 0.8096 (m-80) cc_final: 0.7883 (m-80) REVERT: W 169 GLN cc_start: 0.9298 (tp-100) cc_final: 0.8881 (tp-100) REVERT: W 172 LEU cc_start: 0.8874 (mt) cc_final: 0.8507 (mt) REVERT: W 175 LEU cc_start: 0.8293 (tt) cc_final: 0.7983 (tp) outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 0.2601 time to fit residues: 172.1645 Evaluate side-chains 342 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 152 optimal weight: 0.0770 chunk 350 optimal weight: 6.9990 chunk 396 optimal weight: 50.0000 chunk 319 optimal weight: 5.9990 chunk 476 optimal weight: 8.9990 chunk 190 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 524 optimal weight: 50.0000 chunk 509 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 overall best weight: 2.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 394 ASN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 611 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A 802 ASN A1011 GLN A1173 HIS ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 657 HIS B 958 GLN B1093 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN C 135 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 ASN W 133 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.163554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.139636 restraints weight = 124993.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.141981 restraints weight = 87036.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.143343 restraints weight = 60894.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.144355 restraints weight = 45444.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.144635 restraints weight = 41413.964| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1720 moved from start: 0.7958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 44414 Z= 0.160 Angle : 0.737 35.346 60432 Z= 0.365 Chirality : 0.045 0.231 6856 Planarity : 0.006 0.104 7399 Dihedral : 14.374 77.532 6846 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.25 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.11), residues: 5156 helix: 0.23 (0.12), residues: 1940 sheet: -0.93 (0.18), residues: 801 loop : -1.87 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 967 TYR 0.032 0.002 TYR C 180 PHE 0.040 0.002 PHE A 468 TRP 0.021 0.002 TRP A 185 HIS 0.009 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00352 (44374) covalent geometry : angle 0.69874 (60375) hydrogen bonds : bond 0.03962 ( 1905) hydrogen bonds : angle 5.43048 ( 5345) metal coordination : bond 0.01429 ( 40) metal coordination : angle 7.70455 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.027 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: A 6 TYR cc_start: 0.4284 (p90) cc_final: 0.2905 (m-80) REVERT: A 95 PHE cc_start: 0.5912 (m-10) cc_final: 0.5647 (m-10) REVERT: A 341 MET cc_start: -0.0517 (tpp) cc_final: -0.1541 (tpp) REVERT: A 685 GLU cc_start: 0.8356 (tt0) cc_final: 0.7364 (tm-30) REVERT: A 748 MET cc_start: 0.0679 (ptt) cc_final: -0.0758 (tmm) REVERT: A 849 MET cc_start: 0.6013 (pmm) cc_final: 0.3220 (ttp) REVERT: A 1063 MET cc_start: 0.1494 (mmm) cc_final: 0.1091 (tpp) REVERT: A 1111 MET cc_start: -0.0833 (mmt) cc_final: -0.1248 (mmt) REVERT: A 1187 GLN cc_start: 0.6560 (tm-30) cc_final: 0.6281 (tm-30) REVERT: A 1433 MET cc_start: 0.3174 (tpp) cc_final: 0.2377 (ppp) REVERT: B 110 HIS cc_start: 0.5189 (p90) cc_final: 0.4563 (t70) REVERT: B 346 GLU cc_start: 0.4012 (tm-30) cc_final: 0.2536 (tm-30) REVERT: B 542 MET cc_start: 0.4904 (mtp) cc_final: 0.3363 (ttp) REVERT: B 597 MET cc_start: 0.8273 (ttp) cc_final: 0.7965 (ttp) REVERT: B 601 ARG cc_start: 0.4822 (mmt180) cc_final: 0.4235 (mmt180) REVERT: B 778 MET cc_start: 0.1533 (mtp) cc_final: 0.1141 (mtm) REVERT: B 1072 MET cc_start: -0.0629 (mmt) cc_final: -0.0868 (mmt) REVERT: C 16 ASP cc_start: 0.4692 (t0) cc_final: 0.4486 (t0) REVERT: E 22 MET cc_start: 0.3037 (tpt) cc_final: 0.0851 (mtt) REVERT: E 197 LYS cc_start: 0.6648 (tptp) cc_final: 0.6281 (tptt) REVERT: E 215 MET cc_start: 0.4553 (mtt) cc_final: 0.3821 (mtt) REVERT: F 88 TYR cc_start: 0.1599 (m-80) cc_final: 0.1111 (m-80) REVERT: G 37 SER cc_start: 0.6572 (m) cc_final: 0.6339 (m) REVERT: I 13 MET cc_start: 0.5486 (ppp) cc_final: 0.5218 (ppp) REVERT: L 58 LYS cc_start: 0.5569 (tptt) cc_final: 0.4966 (tptt) REVERT: O 225 GLN cc_start: 0.7297 (tm-30) cc_final: 0.7090 (tm-30) REVERT: W 169 GLN cc_start: 0.9277 (tp-100) cc_final: 0.8899 (tp-100) REVERT: W 172 LEU cc_start: 0.8894 (mt) cc_final: 0.8523 (mt) REVERT: W 176 MET cc_start: 0.7839 (mmp) cc_final: 0.7588 (mmp) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.2756 time to fit residues: 174.2888 Evaluate side-chains 335 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 465 optimal weight: 50.0000 chunk 209 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 420 optimal weight: 7.9990 chunk 402 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 425 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 452 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 654 ASN A 660 ASN A 717 ASN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 HIS B 657 HIS B1065 GLN ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 17 ASN C 184 ASN G 122 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 235 ASN ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 19 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 = 0.4411 r_free = 0.4411 target = 0.166276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.143847 restraints weight = 128102.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.146497 restraints weight = 84004.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.147863 restraints weight = 60653.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.149254 restraints weight = 43415.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.150236 restraints weight = 34237.258| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2054 moved from start: 0.9215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 44414 Z= 0.270 Angle : 1.005 41.791 60432 Z= 0.502 Chirality : 0.053 0.376 6856 Planarity : 0.008 0.112 7399 Dihedral : 14.831 78.752 6846 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.30 % Favored : 91.41 % Rotamer: Outliers : 0.02 % Allowed : 1.13 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.11), residues: 5156 helix: -0.38 (0.12), residues: 1917 sheet: -1.00 (0.18), residues: 792 loop : -2.28 (0.11), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 92 TYR 0.041 0.003 TYR A 404 PHE 0.058 0.004 PHE A 468 TRP 0.025 0.003 TRP B 561 HIS 0.022 0.003 HIS B1104 Details of bonding type rmsd covalent geometry : bond 0.00608 (44374) covalent geometry : angle 0.96152 (60375) hydrogen bonds : bond 0.05598 ( 1905) hydrogen bonds : angle 6.26785 ( 5345) metal coordination : bond 0.01325 ( 40) metal coordination : angle 9.56293 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 1.709 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: A 6 TYR cc_start: 0.4483 (p90) cc_final: 0.2915 (m-80) REVERT: A 341 MET cc_start: -0.0065 (tpp) cc_final: -0.1542 (tpp) REVERT: A 417 TYR cc_start: 0.3694 (m-10) cc_final: 0.2856 (m-80) REVERT: A 437 MET cc_start: 0.4084 (tpt) cc_final: 0.3859 (tpt) REVERT: A 748 MET cc_start: 0.1098 (ptt) cc_final: -0.0381 (tmm) REVERT: A 849 MET cc_start: 0.5736 (pmm) cc_final: 0.3458 (ttm) REVERT: A 1063 MET cc_start: 0.2696 (mmm) cc_final: 0.2253 (tpp) REVERT: A 1111 MET cc_start: -0.0032 (mmt) cc_final: -0.0456 (mmt) REVERT: A 1187 GLN cc_start: 0.6642 (tm-30) cc_final: 0.6348 (tm-30) REVERT: A 1230 GLU cc_start: 0.5358 (pm20) cc_final: 0.4873 (pm20) REVERT: A 1433 MET cc_start: 0.3477 (tpp) cc_final: 0.2527 (ppp) REVERT: B 597 MET cc_start: 0.8439 (ttp) cc_final: 0.8111 (ttp) REVERT: B 601 ARG cc_start: 0.5512 (mmt180) cc_final: 0.4979 (mmt180) REVERT: B 841 MET cc_start: 0.6087 (mpp) cc_final: 0.5870 (mpp) REVERT: B 1072 MET cc_start: -0.0280 (mmt) cc_final: -0.0699 (mmt) REVERT: B 1120 GLU cc_start: 0.2703 (mm-30) cc_final: 0.2475 (tp30) REVERT: C 16 ASP cc_start: 0.5542 (t0) cc_final: 0.5337 (t0) REVERT: D 176 GLU cc_start: 0.6736 (tt0) cc_final: 0.6179 (tp30) REVERT: E 75 MET cc_start: -0.2635 (ttt) cc_final: -0.5540 (mmt) REVERT: E 197 LYS cc_start: 0.6641 (tptp) cc_final: 0.6364 (tptt) REVERT: E 215 MET cc_start: 0.4168 (mtt) cc_final: 0.3631 (mtt) REVERT: G 22 MET cc_start: -0.1825 (mmt) cc_final: -0.2048 (mmt) REVERT: H 7 ASP cc_start: 0.4807 (p0) cc_final: 0.4603 (p0) REVERT: I 13 MET cc_start: 0.5501 (ppp) cc_final: 0.5258 (ppp) REVERT: M 210 MET cc_start: 0.0297 (ptm) cc_final: -0.0237 (tpt) REVERT: O 115 ILE cc_start: 0.7728 (tp) cc_final: 0.7516 (tp) REVERT: W 169 GLN cc_start: 0.9319 (tp-100) cc_final: 0.9002 (tp-100) REVERT: W 172 LEU cc_start: 0.8979 (mt) cc_final: 0.8645 (mt) REVERT: W 175 LEU cc_start: 0.8259 (tp) cc_final: 0.8009 (tp) outliers start: 1 outliers final: 0 residues processed: 405 average time/residue: 0.2753 time to fit residues: 181.0799 Evaluate side-chains 338 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 188 optimal weight: 0.0970 chunk 312 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 168 optimal weight: 30.0000 chunk 461 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 392 optimal weight: 10.0000 chunk 497 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 802 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.165777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.142968 restraints weight = 127175.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.145321 restraints weight = 86243.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.146714 restraints weight = 60662.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.148090 restraints weight = 43518.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.148500 restraints weight = 35084.963| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1908 moved from start: 0.9244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 44414 Z= 0.170 Angle : 0.802 32.952 60432 Z= 0.398 Chirality : 0.047 0.276 6856 Planarity : 0.006 0.142 7399 Dihedral : 14.674 76.821 6846 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.79 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.11), residues: 5156 helix: -0.06 (0.12), residues: 1943 sheet: -1.05 (0.18), residues: 805 loop : -2.13 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 726 TYR 0.031 0.002 TYR B 88 PHE 0.037 0.002 PHE A 468 TRP 0.028 0.002 TRP E 79 HIS 0.013 0.002 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00379 (44374) covalent geometry : angle 0.76231 (60375) hydrogen bonds : bond 0.04370 ( 1905) hydrogen bonds : angle 5.81995 ( 5345) metal coordination : bond 0.01211 ( 40) metal coordination : angle 8.17077 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.632 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: A 6 TYR cc_start: 0.3625 (p90) cc_final: 0.2826 (m-80) REVERT: A 95 PHE cc_start: 0.5890 (m-10) cc_final: 0.5567 (m-10) REVERT: A 146 MET cc_start: -0.0056 (mmp) cc_final: -0.0480 (mmp) REVERT: A 341 MET cc_start: -0.0393 (tpp) cc_final: -0.1591 (tpp) REVERT: A 748 MET cc_start: 0.1042 (ptt) cc_final: -0.0530 (tmm) REVERT: A 849 MET cc_start: 0.5562 (pmm) cc_final: 0.3276 (ttp) REVERT: A 1230 GLU cc_start: 0.5401 (pm20) cc_final: 0.4957 (pm20) REVERT: A 1433 MET cc_start: 0.3122 (tpp) cc_final: 0.2404 (ppp) REVERT: B 522 VAL cc_start: 0.5623 (t) cc_final: 0.5339 (t) REVERT: B 542 MET cc_start: 0.3973 (ttp) cc_final: 0.3691 (ttt) REVERT: B 597 MET cc_start: 0.8547 (ttp) cc_final: 0.8141 (ttp) REVERT: B 601 ARG cc_start: 0.5366 (mmt180) cc_final: 0.4727 (mmt180) REVERT: B 705 MET cc_start: -0.3043 (tpt) cc_final: -0.3734 (tpt) REVERT: B 914 LYS cc_start: 0.3387 (tttt) cc_final: 0.3036 (tmtt) REVERT: B 1072 MET cc_start: -0.0602 (mmt) cc_final: -0.0921 (mmt) REVERT: B 1152 MET cc_start: -0.1577 (mmp) cc_final: -0.1918 (mmp) REVERT: C 16 ASP cc_start: 0.5289 (t0) cc_final: 0.4934 (t0) REVERT: C 75 MET cc_start: -0.3620 (mmm) cc_final: -0.5650 (mmm) REVERT: D 176 GLU cc_start: 0.7019 (tt0) cc_final: 0.6257 (tp30) REVERT: E 22 MET cc_start: 0.2920 (tpt) cc_final: 0.1399 (mtt) REVERT: E 75 MET cc_start: -0.2686 (ttt) cc_final: -0.5559 (mmt) REVERT: E 197 LYS cc_start: 0.6508 (tptp) cc_final: 0.6233 (tptt) REVERT: E 215 MET cc_start: 0.4614 (mtt) cc_final: 0.4016 (mtt) REVERT: G 22 MET cc_start: -0.1991 (mmt) cc_final: -0.2361 (mmt) REVERT: G 37 SER cc_start: 0.6350 (m) cc_final: 0.6124 (m) REVERT: H 7 ASP cc_start: 0.4818 (p0) cc_final: 0.4616 (p0) REVERT: I 13 MET cc_start: 0.5368 (ppp) cc_final: 0.5017 (ppp) REVERT: M 210 MET cc_start: 0.0404 (ptm) cc_final: -0.0239 (tpt) REVERT: M 235 ASN cc_start: 0.4567 (t0) cc_final: 0.4358 (t0) REVERT: Q 393 TYR cc_start: 0.6004 (m-80) cc_final: 0.5249 (m-80) REVERT: W 20 PHE cc_start: 0.7442 (m-80) cc_final: 0.6726 (m-80) REVERT: W 93 HIS cc_start: 0.3844 (m-70) cc_final: 0.3602 (m-70) REVERT: W 123 MET cc_start: -0.1006 (ptt) cc_final: -0.1235 (ppp) REVERT: W 169 GLN cc_start: 0.9303 (tp-100) cc_final: 0.8973 (tp-100) REVERT: W 172 LEU cc_start: 0.9021 (mt) cc_final: 0.8706 (mt) REVERT: W 175 LEU cc_start: 0.8351 (tp) cc_final: 0.8063 (tp) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.2870 time to fit residues: 188.2855 Evaluate side-chains 352 residues out of total 4654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 406 optimal weight: 0.9980 chunk 344 optimal weight: 6.9990 chunk 292 optimal weight: 0.9980 chunk 286 optimal weight: 10.0000 chunk 499 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.166470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.143416 restraints weight = 129991.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.146368 restraints weight = 86031.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.147414 restraints weight = 56915.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.148568 restraints weight = 43297.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.148622 restraints weight = 39654.703| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1954 moved from start: 0.9584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 44414 Z= 0.175 Angle : 0.793 24.806 60432 Z= 0.397 Chirality : 0.047 0.312 6856 Planarity : 0.006 0.091 7399 Dihedral : 14.614 78.382 6846 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.85 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.11), residues: 5156 helix: 0.01 (0.12), residues: 1935 sheet: -1.02 (0.18), residues: 819 loop : -2.05 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 28 TYR 0.029 0.002 TYR C 180 PHE 0.034 0.002 PHE A 468 TRP 0.044 0.003 TRP B 586 HIS 0.018 0.002 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00392 (44374) covalent geometry : angle 0.75876 (60375) hydrogen bonds : bond 0.04390 ( 1905) hydrogen bonds : angle 5.75807 ( 5345) metal coordination : bond 0.01228 ( 40) metal coordination : angle 7.53496 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6164.41 seconds wall clock time: 108 minutes 15.38 seconds (6495.38 seconds total)