Starting phenix.real_space_refine on Tue Aug 26 23:16:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5p_36908/08_2025/8k5p_36908.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5p_36908/08_2025/8k5p_36908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k5p_36908/08_2025/8k5p_36908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5p_36908/08_2025/8k5p_36908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k5p_36908/08_2025/8k5p_36908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5p_36908/08_2025/8k5p_36908.map" } resolution = 2.8 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= -0.001 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 96 5.49 5 Mg 3 5.21 5 S 209 5.16 5 C 26724 2.51 5 N 7413 2.21 5 O 8260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 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: 42713 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1408, 11046 Classifications: {'peptide': 1408} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1341} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 9187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9187 Classifications: {'peptide': 1157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 50, 'TRANS': 1106} Chain breaks: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2125 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "E" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1704 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "H" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1104 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 138} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "I" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 871 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "J" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 895 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "L" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 364 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "N" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 788 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "P" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 430 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 13} Chain: "T" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 770 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "W" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 565 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1455 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 177} Chain breaks: 1 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: {'PTRANS': 8, 'TRANS': 162} Chain: "M" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 6006 Classifications: {'peptide': 744} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 50, 'TRANS': 693} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "O" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2842 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "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: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 797 SG CYS A 107 130.819 72.627 127.704 1.00141.16 S ATOM 821 SG CYS A 110 129.205 75.057 130.092 1.00130.52 S ATOM 1126 SG CYS A 148 133.008 75.180 129.471 1.00142.49 S ATOM 1264 SG CYS A 167 131.479 72.337 131.452 1.00145.75 S ATOM 492 SG CYS A 67 85.957 72.426 107.547 1.00131.21 S ATOM 514 SG CYS A 70 85.267 76.051 106.609 1.00125.56 S ATOM 567 SG CYS A 77 88.080 74.190 104.802 1.00110.90 S ATOM 19740 SG CYS B1163 96.443 85.581 114.299 1.00 91.57 S ATOM 19758 SG CYS B1166 98.615 82.275 114.693 1.00120.57 S ATOM 19883 SG CYS B1182 94.839 82.416 115.392 1.00118.02 S ATOM 19902 SG CYS B1185 97.646 83.982 117.599 1.00114.03 S ATOM 20903 SG CYS C 86 62.727 73.837 40.894 1.00120.39 S ATOM 20920 SG CYS C 88 63.099 71.376 43.794 1.00129.44 S ATOM 20953 SG CYS C 92 61.796 70.245 40.414 1.00105.32 S ATOM 20976 SG CYS C 95 65.481 71.188 40.837 1.00110.38 S ATOM 25891 SG CYS I 7 174.676 37.712 89.208 1.00160.42 S ATOM 25910 SG CYS I 10 171.135 36.198 90.097 1.00164.84 S ATOM 26040 SG CYS I 29 172.307 39.558 91.474 1.00177.54 S ATOM 26064 SG CYS I 32 173.945 36.294 92.595 1.00171.44 S ATOM 26391 SG CYS I 75 169.368 52.693 46.214 1.00133.75 S ATOM 26413 SG CYS I 78 168.975 49.852 43.752 1.00145.95 S ATOM 26613 SG CYS I 103 166.131 50.777 46.097 1.00138.87 S ATOM 26633 SG CYS I 106 169.406 49.046 47.385 1.00144.33 S ATOM 26761 SG CYS J 7 96.144 67.768 33.529 1.00 83.12 S ATOM 26784 SG CYS J 10 94.567 70.196 31.050 1.00 87.28 S ATOM 27064 SG CYS J 45 98.388 69.830 31.287 1.00 92.62 S ATOM 27070 SG CYS J 46 96.144 67.163 29.708 1.00 99.22 S ATOM 28197 SG CYS L 31 83.904 33.994 59.509 1.00128.81 S ATOM 28217 SG CYS L 34 82.620 31.652 56.802 1.00112.40 S ATOM 28321 SG CYS L 48 81.369 31.258 60.340 1.00121.07 S ATOM 28344 SG CYS L 51 84.957 30.342 59.525 1.00132.41 S Time building chain proxies: 8.20, per 1000 atoms: 0.19 Number of scatterers: 42713 At special positions: 0 Unit cell: (205.7, 157.3, 163.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 209 16.00 P 96 15.00 Mg 3 11.99 O 8260 8.00 N 7413 7.00 C 26724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " 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 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " 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 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " 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 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 45 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9646 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 58 sheets defined 39.3% alpha, 15.1% beta 36 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.212A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.502A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.766A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.608A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.638A 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 536 removed outlier: 3.795A pdb=" N CYS A 529 " --> pdb=" O GLN A 525 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.628A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 711 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.719A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.534A pdb=" N ILE A 878 " --> pdb=" O ALA A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.571A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1014 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1127 through 1134 Processing helix chain 'A' and resid 1166 through 1174 Processing helix chain 'A' and resid 1198 through 1202 Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.860A pdb=" N GLY A1213 " --> pdb=" O MET A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1269 removed outlier: 3.599A pdb=" N LYS A1262 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1332 through 1337 removed outlier: 3.938A pdb=" N MET A1336 " --> pdb=" O PHE A1332 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1332 through 1337' Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.856A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1403 removed outlier: 3.844A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1415 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.529A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 28 through 35 removed outlier: 3.858A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 44 through 64 removed outlier: 4.563A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 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: 3.507A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 321 removed outlier: 3.817A pdb=" N LEU B 311 " --> pdb=" O ASP B 307 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.923A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 410 through 436 Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.799A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.812A pdb=" N TRP B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 606 removed outlier: 3.546A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.986A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.788A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.502A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.334A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 811 removed outlier: 3.786A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1016 through 1021 removed outlier: 3.669A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.913A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1063 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 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'B' and resid 1220 through 1224 removed outlier: 4.225A pdb=" N ASP B1223 " --> pdb=" O ARG B1220 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.232A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 270 Processing helix chain 'E' and resid 2 through 27 removed outlier: 3.606A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.685A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.820A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.619A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 4.180A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.532A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 23 Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.504A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.769A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 63 removed outlier: 4.020A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 4.140A pdb=" N LEU K 9 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 53 Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.826A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 809 through 813 removed outlier: 3.766A pdb=" N TYR W 812 " --> pdb=" O SER W 809 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS W 813 " --> pdb=" O ALA W 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 809 through 813' Processing helix chain 'W' and resid 859 through 864 Processing helix chain 'D' and resid 51 through 78 Processing helix chain 'D' and resid 118 through 131 Processing helix chain 'D' and resid 138 through 151 removed outlier: 4.225A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 204 through 220 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'M' and resid 4 through 14 Processing helix chain 'M' and resid 54 through 62 Proline residue: M 60 - end of helix Processing helix chain 'M' and resid 72 through 92 removed outlier: 4.161A pdb=" N MET M 76 " --> pdb=" O THR M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 142 removed outlier: 3.982A pdb=" N MET M 110 " --> pdb=" O PRO M 106 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN M 111 " --> pdb=" O ARG M 107 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN M 112 " --> pdb=" O ALA M 108 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA M 115 " --> pdb=" O ASN M 111 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL M 141 " --> pdb=" O GLN M 137 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY M 142 " --> pdb=" O ARG M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 152 Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'M' and resid 164 through 185 removed outlier: 3.516A pdb=" N ASP M 168 " --> pdb=" O THR M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 189 removed outlier: 3.568A pdb=" N LYS M 189 " --> pdb=" O PRO M 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 186 through 189' Processing helix chain 'M' and resid 205 through 216 Processing helix chain 'M' and resid 234 through 240 removed outlier: 4.300A pdb=" N PHE M 238 " --> pdb=" O ALA M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 244 Processing helix chain 'M' and resid 254 through 259 Processing helix chain 'M' and resid 265 through 271 removed outlier: 3.502A pdb=" N ASP M 268 " --> pdb=" O ASN M 265 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE M 270 " --> pdb=" O LYS M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 285 Processing helix chain 'M' and resid 294 through 305 removed outlier: 3.743A pdb=" N GLU M 299 " --> pdb=" O ASN M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 331 removed outlier: 3.697A pdb=" N ASP M 321 " --> pdb=" O GLU M 317 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP M 322 " --> pdb=" O ARG M 318 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP M 323 " --> pdb=" O ALA M 319 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 359 removed outlier: 4.446A pdb=" N ASP M 349 " --> pdb=" O GLU M 345 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE M 350 " --> pdb=" O ASN M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 404 removed outlier: 3.926A pdb=" N GLY M 389 " --> pdb=" O GLY M 385 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP M 390 " --> pdb=" O SER M 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 593 through 598 removed outlier: 3.768A pdb=" N LYS M 598 " --> pdb=" O ASP M 594 " (cutoff:3.500A) Processing helix chain 'M' and resid 603 through 611 removed outlier: 4.107A pdb=" N ARG M 607 " --> pdb=" O GLY M 603 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR M 609 " --> pdb=" O HIS M 605 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA M 611 " --> pdb=" O ARG M 607 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 645 removed outlier: 3.523A pdb=" N GLU M 621 " --> pdb=" O PRO M 617 " (cutoff:3.500A) Processing helix chain 'M' and resid 681 through 690 Processing helix chain 'M' and resid 699 through 708 Processing helix chain 'M' and resid 713 through 717 Processing helix chain 'M' and resid 730 through 734 removed outlier: 3.631A pdb=" N GLY M 734 " --> pdb=" O SER M 731 " (cutoff:3.500A) Processing helix chain 'M' and resid 742 through 754 Processing helix chain 'M' and resid 758 through 763 Processing helix chain 'M' and resid 764 through 766 No H-bonds generated for 'chain 'M' and resid 764 through 766' Processing helix chain 'M' and resid 780 through 788 Processing helix chain 'M' and resid 873 through 882 Processing helix chain 'M' and resid 885 through 890 removed outlier: 3.968A pdb=" N TYR M 889 " --> pdb=" O ASN M 886 " (cutoff:3.500A) Processing helix chain 'M' and resid 897 through 902 Processing helix chain 'M' and resid 921 through 931 Processing helix chain 'O' and resid 30 through 34 removed outlier: 3.524A pdb=" N GLU O 33 " --> pdb=" O THR O 30 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU O 34 " --> pdb=" O LYS O 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 30 through 34' Processing helix chain 'O' and resid 49 through 55 Processing helix chain 'O' and resid 62 through 66 Processing helix chain 'O' and resid 79 through 93 Processing helix chain 'O' and resid 106 through 114 Processing helix chain 'O' and resid 118 through 122 Processing helix chain 'O' and resid 131 through 134 Processing helix chain 'O' and resid 162 through 175 Processing helix chain 'O' and resid 185 through 192 removed outlier: 3.583A pdb=" N ILE O 189 " --> pdb=" O PRO O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 270 Processing helix chain 'O' and resid 297 through 304 Processing helix chain 'O' and resid 306 through 331 removed outlier: 3.962A pdb=" N CYS O 313 " --> pdb=" O VAL O 309 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU O 314 " --> pdb=" O GLY O 310 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET O 330 " --> pdb=" O TRP O 326 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE O 331 " --> pdb=" O LEU O 327 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 370 removed outlier: 3.514A pdb=" N SER O 366 " --> pdb=" O ASP O 362 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 387 removed outlier: 3.628A pdb=" N LEU O 386 " --> pdb=" O TRP O 382 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS O 387 " --> pdb=" O ARG O 383 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 90 removed outlier: 10.757A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.808A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.501A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.368A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.640A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.126A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB3, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB5, first strand: chain 'A' and resid 1140 through 1141 removed outlier: 4.516A pdb=" N ARG A1274 " --> pdb=" O HIS A1140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1194 through 1195 Processing sheet with id=AB7, first strand: chain 'A' and resid 1224 through 1227 Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.175A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G 9 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AC1, first strand: chain 'B' and resid 92 through 97 removed outlier: 4.656A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 removed outlier: 3.691A pdb=" N HIS B 110 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.291A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.362A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 648 through 651 Processing sheet with id=AC8, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.383A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.597A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.597A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 removed outlier: 5.768A pdb=" N GLY B1042 " --> pdb=" O THR B 805 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 821 through 827 removed outlier: 7.250A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 865 through 866 Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 removed outlier: 4.125A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 939 " --> pdb=" O ILE B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1069 through 1070 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 1172 through 1174 removed outlier: 3.585A pdb=" N ILE B1172 " --> pdb=" O GLU B1181 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B1181 " --> pdb=" O ILE B1172 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.539A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 119 through 120 removed outlier: 7.077A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 48 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.938A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE6, first strand: chain 'E' and resid 58 through 62 removed outlier: 3.527A pdb=" N SER E 59 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER E 77 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE E 109 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.589A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.042A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA H 140 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP H 41 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU H 38 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU H 27 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 15 through 18 Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.704A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS I 108 " --> pdb=" O CYS I 103 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.750A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 837 through 841 removed outlier: 3.798A pdb=" N ASP W 821 " --> pdb=" O THR W 828 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU W 830 " --> pdb=" O VAL W 819 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL W 819 " --> pdb=" O GLU W 830 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.590A pdb=" N LYS G 5 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 99 through 102 removed outlier: 6.552A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.880A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER G 132 " --> pdb=" O ASP G 135 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP G 135 " --> pdb=" O SER G 132 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.654A pdb=" N ARG M 252 " --> pdb=" O LEU M 290 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS M 227 " --> pdb=" O LYS M 249 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU M 251 " --> pdb=" O HIS M 227 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE M 229 " --> pdb=" O LEU M 251 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU M 253 " --> pdb=" O ILE M 229 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU M 50 " --> pdb=" O VAL M 98 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA M 100 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU M 52 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY M 811 " --> pdb=" O PHE M 802 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE M 802 " --> pdb=" O GLY M 811 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 28 through 29 Processing sheet with id=AF9, first strand: chain 'M' and resid 367 through 368 Processing sheet with id=AG1, first strand: chain 'M' and resid 825 through 826 removed outlier: 3.566A pdb=" N ILE M 826 " --> pdb=" O LEU M 838 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU M 838 " --> pdb=" O ILE M 826 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'O' and resid 36 through 37 removed outlier: 6.612A pdb=" N VAL O 206 " --> pdb=" O ILE O 24 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE O 26 " --> pdb=" O ILE O 204 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE O 204 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER O 28 " --> pdb=" O GLU O 202 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU O 202 " --> pdb=" O SER O 28 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR O 203 " --> pdb=" O VAL O 222 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS O 214 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE O 101 " --> pdb=" O ILE O 217 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLY O 219 " --> pdb=" O ILE O 101 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N THR O 103 " --> pdb=" O GLY O 219 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLU O 221 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE O 102 " --> pdb=" O ILE O 137 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU O 126 " --> pdb=" O LEU O 346 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU O 346 " --> pdb=" O LEU O 126 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS O 345 " --> pdb=" O SER O 356 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER O 356 " --> pdb=" O LYS O 345 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 67 through 68 removed outlier: 8.002A pdb=" N LYS O 67 " --> pdb=" O HIS O 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'O' and resid 224 through 225 removed outlier: 3.730A pdb=" N CYS O 224 " --> pdb=" O ALA O 240 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR O 239 " --> pdb=" O ARG O 275 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ILE O 277 " --> pdb=" O TYR O 239 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU O 241 " --> pdb=" O ILE O 277 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLY O 279 " --> pdb=" O GLU O 241 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS O 243 " --> pdb=" O GLY O 279 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LYS O 281 " --> pdb=" O LYS O 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR O 245 " --> pdb=" O LYS O 281 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR O 289 " --> pdb=" O PHE O 280 " (cutoff:3.500A) 1689 hydrogen bonds defined for protein. 4683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 10.58 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7070 1.32 - 1.44: 11627 1.44 - 1.57: 24522 1.57 - 1.70: 189 1.70 - 1.82: 330 Bond restraints: 43738 Sorted by residual: bond pdb=" C PRO F 83 " pdb=" O PRO F 83 " ideal model delta sigma weight residual 1.234 1.193 0.041 1.00e-02 1.00e+04 1.69e+01 bond pdb=" N ILE F 74 " pdb=" CA ILE F 74 " ideal model delta sigma weight residual 1.457 1.490 -0.033 9.00e-03 1.23e+04 1.31e+01 bond pdb=" CA ALA F 105 " pdb=" CB ALA F 105 " ideal model delta sigma weight residual 1.537 1.495 0.042 1.38e-02 5.25e+03 9.44e+00 bond pdb=" CA ALA H 28 " pdb=" CB ALA H 28 " ideal model delta sigma weight residual 1.534 1.488 0.046 1.57e-02 4.06e+03 8.60e+00 bond pdb=" C PRO F 106 " pdb=" O PRO F 106 " ideal model delta sigma weight residual 1.233 1.198 0.035 1.19e-02 7.06e+03 8.55e+00 ... (remaining 43733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 58979 2.63 - 5.25: 492 5.25 - 7.88: 56 7.88 - 10.50: 12 10.50 - 13.13: 5 Bond angle restraints: 59544 Sorted by residual: angle pdb=" N GLN F 78 " pdb=" CA GLN F 78 " pdb=" C GLN F 78 " ideal model delta sigma weight residual 111.81 103.40 8.41 1.54e+00 4.22e-01 2.98e+01 angle pdb=" C ASP H 72 " pdb=" CA ASP H 72 " pdb=" CB ASP H 72 " ideal model delta sigma weight residual 116.54 110.37 6.17 1.15e+00 7.56e-01 2.88e+01 angle pdb=" N THR H 31 " pdb=" CA THR H 31 " pdb=" C THR H 31 " ideal model delta sigma weight residual 112.72 106.70 6.02 1.14e+00 7.69e-01 2.79e+01 angle pdb=" N ASN I 22 " pdb=" CA ASN I 22 " pdb=" C ASN I 22 " ideal model delta sigma weight residual 112.72 106.73 5.99 1.14e+00 7.69e-01 2.76e+01 angle pdb=" CA PRO F 75 " pdb=" C PRO F 75 " pdb=" O PRO F 75 " ideal model delta sigma weight residual 121.31 117.84 3.47 7.40e-01 1.83e+00 2.20e+01 ... (remaining 59539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 25237 35.94 - 71.87: 1161 71.87 - 107.81: 49 107.81 - 143.75: 5 143.75 - 179.68: 4 Dihedral angle restraints: 26456 sinusoidal: 11546 harmonic: 14910 Sorted by residual: dihedral pdb=" CA CYS A1421 " pdb=" C CYS A1421 " pdb=" N ARG A1422 " pdb=" CA ARG A1422 " ideal model delta harmonic sigma weight residual 180.00 159.01 20.99 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" C4' DA T -9 " pdb=" C3' DA T -9 " pdb=" O3' DA T -9 " pdb=" P DA T -8 " ideal model delta sinusoidal sigma weight residual 220.00 40.32 179.68 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA N 1 " pdb=" C3' DA N 1 " pdb=" O3' DA N 1 " pdb=" P DT N 2 " ideal model delta sinusoidal sigma weight residual -140.00 38.40 -178.40 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 26453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 5623 0.054 - 0.108: 893 0.108 - 0.162: 141 0.162 - 0.216: 3 0.216 - 0.270: 3 Chirality restraints: 6663 Sorted by residual: chirality pdb=" CB THR D 26 " pdb=" CA THR D 26 " pdb=" OG1 THR D 26 " pdb=" CG2 THR D 26 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA GLN F 78 " pdb=" N GLN F 78 " pdb=" C GLN F 78 " pdb=" CB GLN F 78 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL F 107 " pdb=" N VAL F 107 " pdb=" C VAL F 107 " pdb=" CB VAL F 107 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 6660 not shown) Planarity restraints: 7380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 786 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ASN B 786 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN B 786 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 787 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 173 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO D 174 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 174 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 174 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 381 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO A 382 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.028 5.00e-02 4.00e+02 ... (remaining 7377 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 754 2.66 - 3.22: 39043 3.22 - 3.78: 67357 3.78 - 4.34: 89117 4.34 - 4.90: 145686 Nonbonded interactions: 341957 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1803 " model vdw 2.104 2.170 nonbonded pdb=" OE2 GLU O 241 " pdb="MG MG O1001 " model vdw 2.109 2.170 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.118 2.170 nonbonded pdb=" N GLU K 79 " pdb=" OE1 GLU K 79 " model vdw 2.188 3.120 nonbonded pdb=" OG1 THR I 55 " pdb=" N ALA I 56 " model vdw 2.196 3.120 ... (remaining 341952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 41.730 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.002 0.048 43770 Z= 0.132 Angle : 0.565 13.131 59589 Z= 0.296 Chirality : 0.041 0.270 6663 Planarity : 0.003 0.059 7380 Dihedral : 18.204 179.684 16810 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.24 % Allowed : 27.01 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.12), residues: 5075 helix: 1.94 (0.13), residues: 1755 sheet: 0.68 (0.20), residues: 776 loop : -0.60 (0.13), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 430 TYR 0.017 0.001 TYR B 666 PHE 0.017 0.001 PHE D 175 TRP 0.011 0.001 TRP A1228 HIS 0.003 0.000 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00250 (43738) covalent geometry : angle 0.55980 (59544) hydrogen bonds : bond 0.17409 ( 1760) hydrogen bonds : angle 6.19366 ( 4861) metal coordination : bond 0.00354 ( 32) metal coordination : angle 2.94882 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 529 time to evaluate : 1.295 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: B 239 GLU cc_start: 0.8713 (pm20) cc_final: 0.8328 (pm20) REVERT: B 430 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7467 (tmm160) REVERT: B 1124 ARG cc_start: 0.8548 (ttm110) cc_final: 0.7965 (mtp85) REVERT: F 112 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8550 (tm-30) REVERT: H 33 GLN cc_start: 0.8676 (mp10) cc_final: 0.8373 (mp10) REVERT: K 54 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8252 (mmm160) REVERT: D 195 ILE cc_start: 0.6674 (mt) cc_final: 0.6470 (mm) REVERT: G 114 LEU cc_start: 0.8001 (mm) cc_final: 0.7796 (mp) REVERT: G 144 ARG cc_start: 0.5868 (ttp-170) cc_final: 0.4719 (mtt90) REVERT: G 171 ILE cc_start: 0.2788 (mt) cc_final: 0.2449 (mp) REVERT: M 366 MET cc_start: 0.4264 (tpp) cc_final: 0.3808 (tpp) REVERT: M 395 ARG cc_start: 0.2711 (mtm110) cc_final: 0.1505 (mtt90) REVERT: M 640 MET cc_start: 0.7515 (mmp) cc_final: 0.7142 (tpt) REVERT: M 707 SER cc_start: 0.5396 (OUTLIER) cc_final: 0.4514 (p) REVERT: M 728 LYS cc_start: -0.0228 (mtmt) cc_final: -0.0442 (tttt) REVERT: O 358 ILE cc_start: 0.2045 (OUTLIER) cc_final: 0.0620 (mt) REVERT: O 365 TYR cc_start: -0.0231 (m-80) cc_final: -0.0685 (t80) outliers start: 100 outliers final: 70 residues processed: 617 average time/residue: 0.6535 time to fit residues: 496.1214 Evaluate side-chains 518 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 446 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1087 PHE Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 707 SER Chi-restraints excluded: chain M residue 899 LEU Chi-restraints excluded: chain M residue 929 GLU Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 358 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 30.0000 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 169 ASN A 299 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN A 493 GLN A 510 GLN A 576 GLN A 587 HIS A 589 GLN A 650 GLN A 742 ASN A 757 ASN A 802 ASN A1011 GLN A1124 HIS ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS A1432 GLN B 60 GLN B 215 GLN B 236 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS B 686 ASN B 716 ASN B 784 ASN B 786 ASN B 862 GLN B 881 ASN B1013 ASN B1062 HIS ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS C 135 GLN E 99 HIS E 106 GLN H 43 ASN H 52 GLN H 71 ASN H 137 GLN H 139 ASN K 2 ASN K 40 HIS K 96 ASN K 104 ASN W 863 ASN D 23 ASN D 41 GLN D 137 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 153 GLN M 55 ASN M 59 HIS M 111 ASN M 125 GLN M 158 ASN M 227 HIS ** M 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN M 265 ASN M 278 GLN M 284 ASN M 396 HIS M 605 HIS M 776 ASN O 179 ASN O 182 GLN O 199 HIS O 305 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.153892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.084592 restraints weight = 79419.495| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.96 r_work: 0.2768 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 43770 Z= 0.414 Angle : 0.737 26.030 59589 Z= 0.374 Chirality : 0.049 0.215 6663 Planarity : 0.005 0.055 7380 Dihedral : 14.216 179.644 6816 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.96 % Allowed : 22.81 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.12), residues: 5075 helix: 1.37 (0.12), residues: 1770 sheet: 0.18 (0.19), residues: 760 loop : -0.79 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 127 TYR 0.029 0.002 TYR B 797 PHE 0.032 0.002 PHE A 219 TRP 0.018 0.002 TRP M 323 HIS 0.011 0.002 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00983 (43738) covalent geometry : angle 0.71346 (59544) hydrogen bonds : bond 0.05921 ( 1760) hydrogen bonds : angle 4.91856 ( 4861) metal coordination : bond 0.01466 ( 32) metal coordination : angle 6.79601 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 453 time to evaluate : 1.433 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: A 68 GLN cc_start: 0.9118 (mp10) cc_final: 0.8880 (mp10) REVERT: A 226 GLU cc_start: 0.9123 (tt0) cc_final: 0.8890 (tm-30) REVERT: A 542 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 771 GLU cc_start: 0.9017 (pt0) cc_final: 0.8746 (pt0) REVERT: A 1078 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8296 (tp-100) REVERT: A 1112 LYS cc_start: 0.9285 (ttpt) cc_final: 0.8731 (mmmm) REVERT: A 1139 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: A 1300 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8697 (mttm) REVERT: A 1337 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8440 (mm-30) REVERT: B 239 GLU cc_start: 0.8776 (pm20) cc_final: 0.7992 (pm20) REVERT: B 241 ARG cc_start: 0.8768 (ttm-80) cc_final: 0.8252 (mtp85) REVERT: B 278 GLN cc_start: 0.7487 (pm20) cc_final: 0.7274 (pm20) REVERT: B 451 LYS cc_start: 0.8231 (ttpp) cc_final: 0.8020 (ttpt) REVERT: B 510 LYS cc_start: 0.8947 (tppp) cc_final: 0.8248 (tmmt) REVERT: B 687 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8228 (tm-30) REVERT: B 862 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8651 (tt0) REVERT: B 864 LYS cc_start: 0.8816 (mmmm) cc_final: 0.8386 (mppt) REVERT: B 1124 ARG cc_start: 0.8862 (ttm110) cc_final: 0.8189 (mtp85) REVERT: B 1125 ASP cc_start: 0.9000 (t0) cc_final: 0.8420 (t0) REVERT: F 76 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8078 (pttp) REVERT: F 78 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7420 (mm-40) REVERT: F 108 PHE cc_start: 0.9389 (m-80) cc_final: 0.9186 (m-80) REVERT: F 110 ASP cc_start: 0.8663 (p0) cc_final: 0.8429 (p0) REVERT: F 112 GLU cc_start: 0.9210 (tm-30) cc_final: 0.8872 (tm-30) REVERT: F 127 GLU cc_start: 0.8958 (pm20) cc_final: 0.8717 (pm20) REVERT: F 138 LEU cc_start: 0.9082 (mm) cc_final: 0.8833 (mt) REVERT: H 33 GLN cc_start: 0.8456 (mp10) cc_final: 0.7980 (mp10) REVERT: I 45 ARG cc_start: 0.8040 (ttt90) cc_final: 0.7567 (tpp80) REVERT: I 47 GLU cc_start: 0.8197 (tp30) cc_final: 0.7579 (tm-30) REVERT: I 48 LEU cc_start: 0.9326 (mm) cc_final: 0.9010 (mm) REVERT: K 22 ASP cc_start: 0.8368 (m-30) cc_final: 0.8141 (m-30) REVERT: K 38 GLU cc_start: 0.8532 (mp0) cc_final: 0.8193 (mp0) REVERT: K 54 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8453 (mmm160) REVERT: L 40 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8489 (pp) REVERT: L 44 ASP cc_start: 0.8595 (t0) cc_final: 0.8277 (t0) REVERT: G 53 ASN cc_start: 0.7554 (t0) cc_final: 0.7332 (t0) REVERT: G 75 ARG cc_start: 0.6721 (ttp80) cc_final: 0.6352 (ptm-80) REVERT: G 114 LEU cc_start: 0.8177 (mm) cc_final: 0.7688 (mp) REVERT: G 144 ARG cc_start: 0.3926 (OUTLIER) cc_final: 0.3591 (mtt90) REVERT: G 171 ILE cc_start: 0.3519 (mt) cc_final: 0.3046 (mp) REVERT: M 14 TYR cc_start: 0.8908 (m-10) cc_final: 0.8569 (m-10) REVERT: M 395 ARG cc_start: 0.3561 (OUTLIER) cc_final: 0.2338 (mtt90) REVERT: M 640 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8079 (tpp) REVERT: M 728 LYS cc_start: 0.0052 (mtmt) cc_final: -0.0341 (tttt) REVERT: M 880 ILE cc_start: 0.7513 (tt) cc_final: 0.7216 (tt) REVERT: O 58 ASP cc_start: 0.2141 (OUTLIER) cc_final: 0.0901 (m-30) REVERT: O 358 ILE cc_start: 0.3371 (OUTLIER) cc_final: 0.2528 (mt) REVERT: O 365 TYR cc_start: -0.0016 (OUTLIER) cc_final: -0.0496 (t80) outliers start: 221 outliers final: 98 residues processed: 624 average time/residue: 0.6384 time to fit residues: 490.1287 Evaluate side-chains 529 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 419 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1300 LYS Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 258 GLN Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 395 ARG Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 640 MET Chi-restraints excluded: chain M residue 646 CYS Chi-restraints excluded: chain M residue 678 THR Chi-restraints excluded: chain M residue 744 ASP Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 895 PHE Chi-restraints excluded: chain M residue 929 GLU Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 358 ILE Chi-restraints excluded: chain O residue 365 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 252 optimal weight: 0.8980 chunk 471 optimal weight: 20.0000 chunk 340 optimal weight: 2.9990 chunk 404 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 484 optimal weight: 40.0000 chunk 316 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS A1387 HIS B 706 GLN B 786 ASN B 881 ASN B1117 GLN H 137 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN ** M 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.161811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092141 restraints weight = 79837.453| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.98 r_work: 0.2830 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43770 Z= 0.132 Angle : 0.576 20.168 59589 Z= 0.289 Chirality : 0.042 0.202 6663 Planarity : 0.004 0.050 7380 Dihedral : 14.049 179.208 6772 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.33 % Favored : 95.65 % Rotamer: Outliers : 3.34 % Allowed : 24.38 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.12), residues: 5075 helix: 1.53 (0.12), residues: 1775 sheet: 0.20 (0.19), residues: 771 loop : -0.75 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 87 TYR 0.035 0.001 TYR M 642 PHE 0.019 0.001 PHE M 328 TRP 0.010 0.001 TRP B 31 HIS 0.005 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00298 (43738) covalent geometry : angle 0.55688 (59544) hydrogen bonds : bond 0.04117 ( 1760) hydrogen bonds : angle 4.53058 ( 4861) metal coordination : bond 0.00657 ( 32) metal coordination : angle 5.43544 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 451 time to evaluate : 1.486 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: A 68 GLN cc_start: 0.9147 (mp10) cc_final: 0.8839 (mp10) REVERT: A 226 GLU cc_start: 0.9106 (tt0) cc_final: 0.8846 (tm-30) REVERT: A 542 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8201 (mm-30) REVERT: A 771 GLU cc_start: 0.8998 (pt0) cc_final: 0.8733 (pt0) REVERT: A 1078 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8319 (tp-100) REVERT: A 1112 LYS cc_start: 0.9267 (ttpt) cc_final: 0.8685 (mmmm) REVERT: A 1139 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: A 1337 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: A 1420 ASP cc_start: 0.8631 (p0) cc_final: 0.8392 (p0) REVERT: A 1454 MET cc_start: 0.8610 (tpt) cc_final: 0.8292 (tpt) REVERT: B 239 GLU cc_start: 0.8683 (pm20) cc_final: 0.7769 (pm20) REVERT: B 241 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8220 (mtp85) REVERT: B 257 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8365 (mttt) REVERT: B 510 LYS cc_start: 0.8863 (tppp) cc_final: 0.8193 (tmmt) REVERT: B 687 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 868 MET cc_start: 0.8089 (tpp) cc_final: 0.7888 (tpp) REVERT: F 110 ASP cc_start: 0.8892 (p0) cc_final: 0.8616 (p0) REVERT: F 112 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8916 (tm-30) REVERT: F 127 GLU cc_start: 0.8904 (pm20) cc_final: 0.8589 (pm20) REVERT: H 33 GLN cc_start: 0.8387 (mp10) cc_final: 0.7964 (mp10) REVERT: I 11 ASN cc_start: 0.7571 (t0) cc_final: 0.6943 (t0) REVERT: I 47 GLU cc_start: 0.8143 (tp30) cc_final: 0.7453 (tm-30) REVERT: I 48 LEU cc_start: 0.9330 (mm) cc_final: 0.8986 (mm) REVERT: K 8 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8295 (mm-30) REVERT: K 24 ASP cc_start: 0.8358 (t0) cc_final: 0.8097 (t0) REVERT: K 38 GLU cc_start: 0.8552 (mp0) cc_final: 0.8061 (pm20) REVERT: L 44 ASP cc_start: 0.8575 (t0) cc_final: 0.8294 (t0) REVERT: G 1 MET cc_start: 0.8093 (tmm) cc_final: 0.7769 (ppp) REVERT: G 44 TYR cc_start: 0.7944 (m-80) cc_final: 0.7728 (m-80) REVERT: G 53 ASN cc_start: 0.7628 (t0) cc_final: 0.7343 (t0) REVERT: G 75 ARG cc_start: 0.6778 (ttp80) cc_final: 0.6384 (ptm160) REVERT: G 114 LEU cc_start: 0.8086 (mm) cc_final: 0.7612 (mp) REVERT: G 144 ARG cc_start: 0.3892 (ttp-170) cc_final: 0.3587 (mtt90) REVERT: G 171 ILE cc_start: 0.3546 (mt) cc_final: 0.3091 (mp) REVERT: M 14 TYR cc_start: 0.8932 (m-10) cc_final: 0.8717 (m-80) REVERT: M 54 MET cc_start: 0.6684 (mmp) cc_final: 0.6476 (mmp) REVERT: M 298 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8424 (ptp-170) REVERT: M 395 ARG cc_start: 0.3143 (OUTLIER) cc_final: 0.1620 (mtt90) REVERT: M 640 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8164 (tpp) REVERT: M 728 LYS cc_start: 0.0108 (mtmt) cc_final: -0.0321 (tptt) REVERT: O 358 ILE cc_start: 0.3434 (OUTLIER) cc_final: 0.2721 (mt) REVERT: O 365 TYR cc_start: -0.0028 (OUTLIER) cc_final: -0.0669 (t80) outliers start: 149 outliers final: 71 residues processed: 561 average time/residue: 0.6575 time to fit residues: 451.2625 Evaluate side-chains 503 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 424 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 298 ARG Chi-restraints excluded: chain M residue 314 PHE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 395 ARG Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 640 MET Chi-restraints excluded: chain M residue 646 CYS Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 895 PHE Chi-restraints excluded: chain M residue 929 GLU Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 292 GLU Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 358 ILE Chi-restraints excluded: chain O residue 365 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 260 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 328 optimal weight: 0.4980 chunk 255 optimal weight: 3.9990 chunk 474 optimal weight: 40.0000 chunk 76 optimal weight: 2.9990 chunk 512 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 313 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN B 881 ASN B 887 HIS H 137 GLN D 39 ASN G 96 GLN M 158 ASN M 192 GLN ** M 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.161781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.092877 restraints weight = 79995.933| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.55 r_work: 0.2805 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 43770 Z= 0.160 Angle : 0.565 18.987 59589 Z= 0.285 Chirality : 0.042 0.193 6663 Planarity : 0.004 0.048 7380 Dihedral : 14.001 178.711 6758 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.73 % Favored : 95.25 % Rotamer: Outliers : 3.32 % Allowed : 24.16 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.12), residues: 5075 helix: 1.61 (0.13), residues: 1775 sheet: 0.20 (0.19), residues: 771 loop : -0.73 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 87 TYR 0.027 0.001 TYR M 300 PHE 0.022 0.001 PHE A 219 TRP 0.028 0.001 TRP M 188 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00371 (43738) covalent geometry : angle 0.54695 (59544) hydrogen bonds : bond 0.03950 ( 1760) hydrogen bonds : angle 4.37357 ( 4861) metal coordination : bond 0.00656 ( 32) metal coordination : angle 5.16803 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 442 time to evaluate : 1.703 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: A 68 GLN cc_start: 0.9157 (mp10) cc_final: 0.8823 (mp10) REVERT: A 226 GLU cc_start: 0.9126 (tt0) cc_final: 0.8854 (tm-30) REVERT: A 618 GLU cc_start: 0.7907 (pm20) cc_final: 0.7651 (pm20) REVERT: A 771 GLU cc_start: 0.9083 (pt0) cc_final: 0.8801 (pt0) REVERT: A 1078 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8369 (tp-100) REVERT: A 1112 LYS cc_start: 0.9283 (ttpt) cc_final: 0.8705 (mmmm) REVERT: A 1139 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6782 (tp30) REVERT: A 1337 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: A 1420 ASP cc_start: 0.8634 (p0) cc_final: 0.8383 (p0) REVERT: A 1454 MET cc_start: 0.8574 (tpt) cc_final: 0.8240 (tpt) REVERT: B 239 GLU cc_start: 0.8724 (pm20) cc_final: 0.7666 (pm20) REVERT: B 241 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8265 (mtm110) REVERT: B 510 LYS cc_start: 0.8805 (tppp) cc_final: 0.8131 (tmmt) REVERT: B 687 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 868 MET cc_start: 0.8114 (tpp) cc_final: 0.7853 (tpp) REVERT: B 1111 MET cc_start: 0.9222 (mmm) cc_final: 0.8863 (mmm) REVERT: F 110 ASP cc_start: 0.8991 (p0) cc_final: 0.8705 (p0) REVERT: F 112 GLU cc_start: 0.9307 (tm-30) cc_final: 0.8943 (tm-30) REVERT: F 127 GLU cc_start: 0.8928 (pm20) cc_final: 0.8607 (pm20) REVERT: H 33 GLN cc_start: 0.8324 (mp10) cc_final: 0.7916 (mp10) REVERT: I 11 ASN cc_start: 0.7536 (t0) cc_final: 0.6818 (t0) REVERT: I 47 GLU cc_start: 0.8213 (tp30) cc_final: 0.7560 (tm-30) REVERT: I 48 LEU cc_start: 0.9322 (mm) cc_final: 0.8990 (mm) REVERT: K 8 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8341 (mm-30) REVERT: K 24 ASP cc_start: 0.8452 (t0) cc_final: 0.8166 (t0) REVERT: K 38 GLU cc_start: 0.8551 (mp0) cc_final: 0.8068 (pm20) REVERT: L 40 LEU cc_start: 0.8453 (pp) cc_final: 0.8164 (pt) REVERT: L 44 ASP cc_start: 0.8668 (t0) cc_final: 0.8250 (t0) REVERT: G 1 MET cc_start: 0.8025 (tmm) cc_final: 0.7744 (ppp) REVERT: G 53 ASN cc_start: 0.7790 (t0) cc_final: 0.7436 (t0) REVERT: G 75 ARG cc_start: 0.6817 (ttp80) cc_final: 0.6329 (ptm160) REVERT: G 114 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7597 (mp) REVERT: G 144 ARG cc_start: 0.3847 (OUTLIER) cc_final: 0.3612 (mtt90) REVERT: G 171 ILE cc_start: 0.3551 (mt) cc_final: 0.3084 (mp) REVERT: M 14 TYR cc_start: 0.8914 (m-10) cc_final: 0.8452 (m-10) REVERT: M 54 MET cc_start: 0.6871 (mmp) cc_final: 0.6616 (mmp) REVERT: M 298 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8444 (ptp-170) REVERT: M 395 ARG cc_start: 0.3380 (mtm110) cc_final: 0.1919 (mtt90) REVERT: M 640 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8285 (tpp) REVERT: M 728 LYS cc_start: 0.0219 (mtmt) cc_final: -0.0279 (tptt) REVERT: O 58 ASP cc_start: 0.1927 (OUTLIER) cc_final: 0.0640 (m-30) REVERT: O 127 ARG cc_start: 0.5032 (OUTLIER) cc_final: 0.4751 (mpp-170) REVERT: O 358 ILE cc_start: 0.3240 (OUTLIER) cc_final: 0.2624 (mt) REVERT: O 365 TYR cc_start: 0.0008 (OUTLIER) cc_final: -0.0623 (t80) outliers start: 148 outliers final: 85 residues processed: 559 average time/residue: 0.6704 time to fit residues: 459.2650 Evaluate side-chains 519 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 424 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1185 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 298 ARG Chi-restraints excluded: chain M residue 314 PHE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 640 MET Chi-restraints excluded: chain M residue 646 CYS Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 895 PHE Chi-restraints excluded: chain M residue 899 LEU Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 127 ARG Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 292 GLU Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 358 ILE Chi-restraints excluded: chain O residue 365 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 196 optimal weight: 2.9990 chunk 391 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 414 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 489 optimal weight: 30.0000 chunk 79 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 ASN A1110 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN B 881 ASN H 137 GLN D 28 GLN D 39 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 804 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.161655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092549 restraints weight = 79204.877| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.95 r_work: 0.2833 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43770 Z= 0.160 Angle : 0.578 18.584 59589 Z= 0.288 Chirality : 0.042 0.358 6663 Planarity : 0.004 0.049 7380 Dihedral : 13.968 178.557 6747 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 3.66 % Allowed : 23.98 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.12), residues: 5075 helix: 1.63 (0.13), residues: 1767 sheet: 0.20 (0.19), residues: 773 loop : -0.72 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 87 TYR 0.023 0.001 TYR M 300 PHE 0.022 0.001 PHE A 219 TRP 0.010 0.001 TRP B 31 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00375 (43738) covalent geometry : angle 0.56046 (59544) hydrogen bonds : bond 0.03863 ( 1760) hydrogen bonds : angle 4.29802 ( 4861) metal coordination : bond 0.00631 ( 32) metal coordination : angle 5.11175 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 444 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9105 (mp10) cc_final: 0.8881 (mp10) REVERT: A 226 GLU cc_start: 0.9078 (tt0) cc_final: 0.8832 (tm-30) REVERT: A 771 GLU cc_start: 0.9084 (pt0) cc_final: 0.8827 (pt0) REVERT: A 826 ASP cc_start: 0.8707 (m-30) cc_final: 0.8168 (t0) REVERT: A 1078 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8372 (tp-100) REVERT: A 1112 LYS cc_start: 0.9269 (mtpt) cc_final: 0.8680 (mmmm) REVERT: A 1287 TYR cc_start: 0.8340 (m-10) cc_final: 0.8084 (m-10) REVERT: A 1337 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: A 1420 ASP cc_start: 0.8562 (p0) cc_final: 0.8306 (p0) REVERT: A 1454 MET cc_start: 0.8500 (tpt) cc_final: 0.8168 (tpt) REVERT: B 239 GLU cc_start: 0.8761 (pm20) cc_final: 0.7689 (pm20) REVERT: B 241 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8263 (mtm110) REVERT: B 278 GLN cc_start: 0.7606 (pm20) cc_final: 0.7318 (pm20) REVERT: B 510 LYS cc_start: 0.8835 (tppp) cc_final: 0.8213 (tmmt) REVERT: B 687 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 816 GLU cc_start: 0.8727 (mp0) cc_final: 0.8479 (mp0) REVERT: B 868 MET cc_start: 0.8200 (tpp) cc_final: 0.7928 (tpp) REVERT: B 889 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8582 (t) REVERT: B 1111 MET cc_start: 0.9193 (mmm) cc_final: 0.8809 (mmm) REVERT: B 1181 GLU cc_start: 0.8212 (pm20) cc_final: 0.7869 (mp0) REVERT: F 110 ASP cc_start: 0.9044 (p0) cc_final: 0.8757 (p0) REVERT: F 112 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8856 (tm-30) REVERT: F 127 GLU cc_start: 0.8901 (pm20) cc_final: 0.8574 (pm20) REVERT: H 33 GLN cc_start: 0.8346 (mp10) cc_final: 0.7931 (mp10) REVERT: I 11 ASN cc_start: 0.7483 (t0) cc_final: 0.6740 (t0) REVERT: I 47 GLU cc_start: 0.8213 (tp30) cc_final: 0.7538 (tm-30) REVERT: I 48 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8981 (mm) REVERT: K 8 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8325 (mm-30) REVERT: K 24 ASP cc_start: 0.8456 (t0) cc_final: 0.8186 (t0) REVERT: K 36 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8286 (mm-30) REVERT: K 38 GLU cc_start: 0.8509 (mp0) cc_final: 0.7982 (pm20) REVERT: L 44 ASP cc_start: 0.8696 (t0) cc_final: 0.8311 (t0) REVERT: G 22 MET cc_start: 0.8000 (ptt) cc_final: 0.7716 (ptt) REVERT: G 25 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7952 (t80) REVERT: G 53 ASN cc_start: 0.7898 (t0) cc_final: 0.7479 (t0) REVERT: G 114 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7622 (mp) REVERT: G 144 ARG cc_start: 0.3796 (OUTLIER) cc_final: 0.3517 (mtt90) REVERT: M 54 MET cc_start: 0.7183 (mmp) cc_final: 0.6834 (mmp) REVERT: M 209 MET cc_start: 0.8157 (pp-130) cc_final: 0.7897 (ppp) REVERT: M 298 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8393 (ptt-90) REVERT: M 395 ARG cc_start: 0.3315 (mtm110) cc_final: 0.2006 (mtt180) REVERT: M 640 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8214 (tpp) REVERT: M 728 LYS cc_start: 0.0185 (mtmt) cc_final: -0.0300 (tptt) REVERT: M 735 ILE cc_start: 0.3422 (OUTLIER) cc_final: 0.3213 (mt) REVERT: M 850 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5142 (mp) REVERT: O 127 ARG cc_start: 0.5031 (OUTLIER) cc_final: 0.4727 (mpp-170) REVERT: O 358 ILE cc_start: 0.3163 (OUTLIER) cc_final: 0.2378 (mt) REVERT: O 365 TYR cc_start: -0.0043 (OUTLIER) cc_final: -0.0854 (t80) outliers start: 163 outliers final: 92 residues processed: 567 average time/residue: 0.6439 time to fit residues: 448.6550 Evaluate side-chains 527 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 421 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1185 CYS Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 298 ARG Chi-restraints excluded: chain M residue 314 PHE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 640 MET Chi-restraints excluded: chain M residue 735 ILE Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 850 LEU Chi-restraints excluded: chain M residue 895 PHE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 127 ARG Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 358 ILE Chi-restraints excluded: chain O residue 365 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 257 optimal weight: 1.9990 chunk 452 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 chunk 445 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 ASN A1110 ASN B 706 GLN B 786 ASN B 881 ASN H 137 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.162015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092917 restraints weight = 79905.002| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.96 r_work: 0.2831 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 43770 Z= 0.138 Angle : 0.575 17.342 59589 Z= 0.286 Chirality : 0.042 0.361 6663 Planarity : 0.004 0.050 7380 Dihedral : 13.947 178.244 6746 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.69 % Favored : 95.29 % Rotamer: Outliers : 3.48 % Allowed : 24.32 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.12), residues: 5075 helix: 1.67 (0.13), residues: 1765 sheet: 0.20 (0.19), residues: 777 loop : -0.68 (0.13), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 87 TYR 0.030 0.001 TYR M 300 PHE 0.021 0.001 PHE A 219 TRP 0.009 0.001 TRP B 31 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00320 (43738) covalent geometry : angle 0.55921 (59544) hydrogen bonds : bond 0.03633 ( 1760) hydrogen bonds : angle 4.22348 ( 4861) metal coordination : bond 0.00563 ( 32) metal coordination : angle 4.95203 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 447 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9392 (mp) cc_final: 0.8884 (pp) REVERT: A 68 GLN cc_start: 0.9116 (mp10) cc_final: 0.8778 (mp10) REVERT: A 618 GLU cc_start: 0.8000 (pm20) cc_final: 0.7672 (pm20) REVERT: A 771 GLU cc_start: 0.9084 (pt0) cc_final: 0.8812 (pt0) REVERT: A 826 ASP cc_start: 0.8707 (m-30) cc_final: 0.8189 (t0) REVERT: A 1078 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8306 (tp-100) REVERT: A 1112 LYS cc_start: 0.9275 (mtpt) cc_final: 0.8700 (mmmm) REVERT: A 1139 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6875 (tp30) REVERT: A 1228 TRP cc_start: 0.6938 (m-90) cc_final: 0.6668 (m-90) REVERT: A 1287 TYR cc_start: 0.8342 (m-10) cc_final: 0.8087 (m-10) REVERT: A 1337 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: A 1420 ASP cc_start: 0.8531 (p0) cc_final: 0.8272 (p0) REVERT: A 1454 MET cc_start: 0.8564 (tpt) cc_final: 0.8230 (tpt) REVERT: B 239 GLU cc_start: 0.8740 (pm20) cc_final: 0.7678 (pm20) REVERT: B 241 ARG cc_start: 0.8639 (ttm-80) cc_final: 0.8222 (mtm110) REVERT: B 391 ASP cc_start: 0.7893 (p0) cc_final: 0.7688 (p0) REVERT: B 396 ASP cc_start: 0.8745 (m-30) cc_final: 0.8370 (m-30) REVERT: B 510 LYS cc_start: 0.8823 (tppp) cc_final: 0.8202 (tmmt) REVERT: B 687 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8095 (tm-30) REVERT: B 816 GLU cc_start: 0.8729 (mp0) cc_final: 0.8470 (mp0) REVERT: B 868 MET cc_start: 0.8240 (tpp) cc_final: 0.7998 (tpp) REVERT: B 1111 MET cc_start: 0.9120 (mmm) cc_final: 0.8708 (mmm) REVERT: B 1125 ASP cc_start: 0.8917 (t0) cc_final: 0.8325 (t0) REVERT: C 12 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8060 (tm-30) REVERT: F 110 ASP cc_start: 0.9060 (p0) cc_final: 0.8764 (p0) REVERT: F 112 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8908 (tm-30) REVERT: H 33 GLN cc_start: 0.8289 (mp10) cc_final: 0.7870 (mp10) REVERT: H 67 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7906 (OUTLIER) REVERT: H 135 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8166 (pp) REVERT: I 11 ASN cc_start: 0.7535 (t0) cc_final: 0.6748 (t0) REVERT: I 47 GLU cc_start: 0.8181 (tp30) cc_final: 0.7437 (tm-30) REVERT: I 48 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8959 (mm) REVERT: K 8 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8330 (mm-30) REVERT: K 24 ASP cc_start: 0.8474 (t0) cc_final: 0.8196 (t0) REVERT: K 36 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8206 (mm-30) REVERT: K 38 GLU cc_start: 0.8505 (mp0) cc_final: 0.7951 (pm20) REVERT: L 40 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8067 (pp) REVERT: L 44 ASP cc_start: 0.8649 (t0) cc_final: 0.8336 (t0) REVERT: G 1 MET cc_start: 0.8178 (tmm) cc_final: 0.7862 (ppp) REVERT: G 25 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7957 (t80) REVERT: G 53 ASN cc_start: 0.8112 (t0) cc_final: 0.7773 (t0) REVERT: G 75 ARG cc_start: 0.7025 (ttp80) cc_final: 0.6506 (ptm160) REVERT: G 114 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7622 (mp) REVERT: G 144 ARG cc_start: 0.4015 (OUTLIER) cc_final: 0.3628 (mtt90) REVERT: M 54 MET cc_start: 0.7206 (mmp) cc_final: 0.6850 (mmp) REVERT: M 395 ARG cc_start: 0.3366 (mtm110) cc_final: 0.2078 (mtt-85) REVERT: M 640 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8225 (tpp) REVERT: M 728 LYS cc_start: 0.0318 (mtmt) cc_final: -0.0393 (tttt) REVERT: M 894 ASN cc_start: 0.4737 (OUTLIER) cc_final: 0.2259 (p0) REVERT: O 358 ILE cc_start: 0.3225 (OUTLIER) cc_final: 0.2487 (mt) REVERT: O 365 TYR cc_start: -0.0017 (OUTLIER) cc_final: -0.0866 (t80) outliers start: 155 outliers final: 89 residues processed: 558 average time/residue: 0.6701 time to fit residues: 459.8097 Evaluate side-chains 531 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 429 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 322 PHE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1185 CYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 314 PHE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 640 MET Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 894 ASN Chi-restraints excluded: chain M residue 929 GLU Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 127 ARG Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 358 ILE Chi-restraints excluded: chain O residue 365 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 436 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 460 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 475 optimal weight: 9.9990 chunk 326 optimal weight: 5.9990 chunk 209 optimal weight: 0.5980 chunk 291 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS A1110 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN B 881 ASN H 137 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 HIS M 258 GLN M 287 GLN M 332 ASN O 352 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.156208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087584 restraints weight = 78275.513| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.93 r_work: 0.2828 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 43770 Z= 0.177 Angle : 0.596 18.443 59589 Z= 0.296 Chirality : 0.043 0.363 6663 Planarity : 0.004 0.054 7380 Dihedral : 13.970 178.374 6739 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.73 % Favored : 95.25 % Rotamer: Outliers : 3.66 % Allowed : 24.45 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.12), residues: 5075 helix: 1.62 (0.12), residues: 1773 sheet: 0.22 (0.19), residues: 768 loop : -0.73 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 175 TYR 0.031 0.001 TYR M 300 PHE 0.023 0.001 PHE A 219 TRP 0.009 0.001 TRP B 31 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00417 (43738) covalent geometry : angle 0.57852 (59544) hydrogen bonds : bond 0.03889 ( 1760) hydrogen bonds : angle 4.23096 ( 4861) metal coordination : bond 0.00687 ( 32) metal coordination : angle 5.24426 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 423 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 618 GLU cc_start: 0.8094 (pm20) cc_final: 0.7729 (pm20) REVERT: A 771 GLU cc_start: 0.9147 (pt0) cc_final: 0.8888 (pt0) REVERT: A 826 ASP cc_start: 0.8712 (m-30) cc_final: 0.8207 (t0) REVERT: A 1078 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8339 (tp-100) REVERT: A 1112 LYS cc_start: 0.9282 (mtpt) cc_final: 0.8718 (mmmm) REVERT: A 1139 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: A 1228 TRP cc_start: 0.7026 (m-90) cc_final: 0.6728 (m-90) REVERT: A 1337 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: A 1420 ASP cc_start: 0.8544 (p0) cc_final: 0.8318 (p0) REVERT: A 1454 MET cc_start: 0.8515 (tpt) cc_final: 0.8180 (tpt) REVERT: B 239 GLU cc_start: 0.8750 (pm20) cc_final: 0.7696 (pm20) REVERT: B 241 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8184 (mtp85) REVERT: B 396 ASP cc_start: 0.8740 (m-30) cc_final: 0.8307 (m-30) REVERT: B 510 LYS cc_start: 0.8864 (tppp) cc_final: 0.8227 (tmmt) REVERT: B 687 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8053 (tm-30) REVERT: B 816 GLU cc_start: 0.8734 (mp0) cc_final: 0.8467 (mp0) REVERT: B 868 MET cc_start: 0.8298 (tpp) cc_final: 0.8080 (tpp) REVERT: B 1111 MET cc_start: 0.9094 (mmm) cc_final: 0.8743 (mmm) REVERT: B 1120 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8160 (tp30) REVERT: B 1125 ASP cc_start: 0.8934 (t0) cc_final: 0.8401 (t0) REVERT: B 1181 GLU cc_start: 0.8130 (pm20) cc_final: 0.7927 (mp0) REVERT: C 12 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8158 (tm-30) REVERT: F 110 ASP cc_start: 0.9061 (p0) cc_final: 0.8747 (p0) REVERT: F 112 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8855 (tm-30) REVERT: F 127 GLU cc_start: 0.9012 (pm20) cc_final: 0.8739 (pm20) REVERT: H 33 GLN cc_start: 0.8265 (mp10) cc_final: 0.7837 (mp10) REVERT: H 67 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7972 (p0) REVERT: H 135 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8210 (pp) REVERT: I 11 ASN cc_start: 0.7593 (t0) cc_final: 0.6779 (t0) REVERT: I 47 GLU cc_start: 0.8190 (tp30) cc_final: 0.7484 (tm-30) REVERT: I 48 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8980 (mm) REVERT: K 8 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8308 (mm-30) REVERT: K 24 ASP cc_start: 0.8475 (t0) cc_final: 0.8194 (t0) REVERT: K 36 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8216 (mm-30) REVERT: K 38 GLU cc_start: 0.8465 (mp0) cc_final: 0.7877 (pm20) REVERT: L 40 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8112 (pp) REVERT: L 44 ASP cc_start: 0.8681 (t0) cc_final: 0.8292 (t0) REVERT: W 808 ARG cc_start: 0.6102 (ptp90) cc_final: 0.5862 (pmm-80) REVERT: G 1 MET cc_start: 0.8260 (tmm) cc_final: 0.7991 (ppp) REVERT: G 25 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7962 (t80) REVERT: G 49 LEU cc_start: 0.9020 (pp) cc_final: 0.8414 (pt) REVERT: G 53 ASN cc_start: 0.8246 (t0) cc_final: 0.7866 (t0) REVERT: G 75 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6735 (ptm160) REVERT: G 114 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7677 (mp) REVERT: G 144 ARG cc_start: 0.3917 (OUTLIER) cc_final: 0.3560 (mtt90) REVERT: M 54 MET cc_start: 0.7501 (mmp) cc_final: 0.7156 (mmp) REVERT: M 109 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8264 (tppp) REVERT: M 258 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: M 298 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8336 (ptt-90) REVERT: M 395 ARG cc_start: 0.3344 (mtm110) cc_final: 0.2105 (mtt-85) REVERT: M 640 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8295 (tpp) REVERT: M 665 HIS cc_start: 0.4641 (OUTLIER) cc_final: 0.4272 (p-80) REVERT: M 728 LYS cc_start: 0.0149 (mtmt) cc_final: -0.0320 (tptt) REVERT: M 738 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4669 (tm) REVERT: M 850 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5279 (mp) REVERT: M 894 ASN cc_start: 0.4539 (OUTLIER) cc_final: 0.4125 (p0) REVERT: O 358 ILE cc_start: 0.2999 (OUTLIER) cc_final: 0.2147 (mt) REVERT: O 365 TYR cc_start: 0.0012 (OUTLIER) cc_final: -0.0870 (t80) outliers start: 163 outliers final: 104 residues processed: 549 average time/residue: 0.6763 time to fit residues: 454.2737 Evaluate side-chains 536 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 412 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1185 CYS Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 258 GLN Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 298 ARG Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 314 PHE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 599 LEU Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 640 MET Chi-restraints excluded: chain M residue 646 CYS Chi-restraints excluded: chain M residue 665 HIS Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 850 LEU Chi-restraints excluded: chain M residue 894 ASN Chi-restraints excluded: chain M residue 899 LEU Chi-restraints excluded: chain M residue 929 GLU Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 127 ARG Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 358 ILE Chi-restraints excluded: chain O residue 365 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 510 optimal weight: 30.0000 chunk 52 optimal weight: 0.9990 chunk 346 optimal weight: 0.3980 chunk 184 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 406 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 429 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS A1110 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 881 ASN H 137 GLN D 39 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.156618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088085 restraints weight = 78693.276| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.95 r_work: 0.2848 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43770 Z= 0.138 Angle : 0.589 17.145 59589 Z= 0.292 Chirality : 0.042 0.377 6663 Planarity : 0.004 0.053 7380 Dihedral : 13.952 178.107 6739 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 3.28 % Allowed : 25.21 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.12), residues: 5075 helix: 1.68 (0.13), residues: 1765 sheet: 0.20 (0.19), residues: 783 loop : -0.68 (0.13), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 175 TYR 0.030 0.001 TYR M 300 PHE 0.021 0.001 PHE A 219 TRP 0.009 0.001 TRP B 31 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00318 (43738) covalent geometry : angle 0.57264 (59544) hydrogen bonds : bond 0.03597 ( 1760) hydrogen bonds : angle 4.16660 ( 4861) metal coordination : bond 0.00554 ( 32) metal coordination : angle 4.98518 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 432 time to evaluate : 1.352 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: A 65 LEU cc_start: 0.9399 (mp) cc_final: 0.8929 (pp) REVERT: A 68 GLN cc_start: 0.9028 (mp10) cc_final: 0.8653 (mp10) REVERT: A 618 GLU cc_start: 0.8086 (pm20) cc_final: 0.7707 (pm20) REVERT: A 771 GLU cc_start: 0.9141 (pt0) cc_final: 0.8873 (pt0) REVERT: A 826 ASP cc_start: 0.8695 (m-30) cc_final: 0.8188 (t0) REVERT: A 1078 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8388 (tp-100) REVERT: A 1112 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8699 (mmmm) REVERT: A 1139 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: A 1228 TRP cc_start: 0.7003 (m-90) cc_final: 0.6755 (m-90) REVERT: A 1312 ASN cc_start: 0.8198 (t0) cc_final: 0.7473 (t0) REVERT: A 1337 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: A 1420 ASP cc_start: 0.8523 (p0) cc_final: 0.8296 (p0) REVERT: A 1454 MET cc_start: 0.8513 (tpt) cc_final: 0.8205 (tpt) REVERT: B 90 ILE cc_start: 0.7758 (mm) cc_final: 0.7448 (mp) REVERT: B 239 GLU cc_start: 0.8736 (pm20) cc_final: 0.7673 (pm20) REVERT: B 241 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8153 (mtp85) REVERT: B 396 ASP cc_start: 0.8731 (m-30) cc_final: 0.8304 (m-30) REVERT: B 510 LYS cc_start: 0.8840 (tppp) cc_final: 0.8206 (tmmt) REVERT: B 687 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8058 (tm-30) REVERT: B 816 GLU cc_start: 0.8750 (mp0) cc_final: 0.8473 (mp0) REVERT: B 862 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: B 868 MET cc_start: 0.8315 (tpp) cc_final: 0.8031 (tpp) REVERT: B 1111 MET cc_start: 0.9075 (mmm) cc_final: 0.8732 (mmm) REVERT: B 1120 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8074 (tp30) REVERT: B 1125 ASP cc_start: 0.8923 (t0) cc_final: 0.8326 (t0) REVERT: C 12 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8161 (tm-30) REVERT: F 110 ASP cc_start: 0.9073 (p0) cc_final: 0.8749 (p0) REVERT: F 111 LEU cc_start: 0.9323 (mt) cc_final: 0.9098 (mp) REVERT: F 112 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8820 (tm-30) REVERT: F 127 GLU cc_start: 0.8976 (pm20) cc_final: 0.8711 (pm20) REVERT: H 67 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8001 (p0) REVERT: H 135 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8215 (pp) REVERT: I 11 ASN cc_start: 0.7693 (t0) cc_final: 0.6831 (t0) REVERT: I 47 GLU cc_start: 0.8243 (tp30) cc_final: 0.7454 (tm-30) REVERT: I 48 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8983 (mm) REVERT: K 8 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8308 (mm-30) REVERT: K 24 ASP cc_start: 0.8512 (t0) cc_final: 0.8205 (t0) REVERT: K 36 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8072 (mm-30) REVERT: K 38 GLU cc_start: 0.8460 (mp0) cc_final: 0.7863 (pm20) REVERT: L 44 ASP cc_start: 0.8702 (t0) cc_final: 0.8320 (t0) REVERT: W 808 ARG cc_start: 0.6069 (ptp90) cc_final: 0.5796 (pmm-80) REVERT: G 1 MET cc_start: 0.8321 (tmm) cc_final: 0.8069 (ppp) REVERT: G 25 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7958 (t80) REVERT: G 53 ASN cc_start: 0.8146 (t0) cc_final: 0.7926 (t0) REVERT: G 75 ARG cc_start: 0.7211 (ttp80) cc_final: 0.6696 (ptm160) REVERT: G 114 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7708 (mp) REVERT: G 144 ARG cc_start: 0.3862 (OUTLIER) cc_final: 0.3599 (mtt90) REVERT: M 54 MET cc_start: 0.7635 (mmp) cc_final: 0.7267 (mmp) REVERT: M 109 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8245 (tppp) REVERT: M 258 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6676 (mp10) REVERT: M 395 ARG cc_start: 0.3285 (mtm110) cc_final: 0.2036 (mtt-85) REVERT: M 640 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: M 665 HIS cc_start: 0.4498 (OUTLIER) cc_final: 0.4026 (p-80) REVERT: M 728 LYS cc_start: 0.0263 (mtmt) cc_final: -0.0407 (tttt) REVERT: M 850 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5330 (mp) REVERT: O 358 ILE cc_start: 0.2972 (OUTLIER) cc_final: 0.2101 (mt) REVERT: O 365 TYR cc_start: 0.0063 (OUTLIER) cc_final: -0.0847 (t80) outliers start: 146 outliers final: 98 residues processed: 544 average time/residue: 0.6491 time to fit residues: 433.2388 Evaluate side-chains 530 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 415 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1110 ASN Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1185 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 144 ARG Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 258 GLN Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 314 PHE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 599 LEU Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 640 MET Chi-restraints excluded: chain M residue 646 CYS Chi-restraints excluded: chain M residue 665 HIS Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 850 LEU Chi-restraints excluded: chain M residue 899 LEU Chi-restraints excluded: chain M residue 929 GLU Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 127 ARG Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 358 ILE Chi-restraints excluded: chain O residue 365 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 510 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 157 optimal weight: 0.0170 chunk 506 optimal weight: 9.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 881 ASN B 887 HIS H 137 GLN D 28 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.156323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087304 restraints weight = 77920.251| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.98 r_work: 0.2830 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43770 Z= 0.188 Angle : 0.621 18.118 59589 Z= 0.308 Chirality : 0.043 0.375 6663 Planarity : 0.004 0.059 7380 Dihedral : 13.964 178.278 6738 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.83 % Favored : 95.15 % Rotamer: Outliers : 3.12 % Allowed : 25.55 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.12), residues: 5075 helix: 1.58 (0.12), residues: 1779 sheet: 0.22 (0.19), residues: 764 loop : -0.76 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 175 TYR 0.026 0.001 TYR M 300 PHE 0.024 0.001 PHE A 219 TRP 0.009 0.001 TRP B 31 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00443 (43738) covalent geometry : angle 0.60393 (59544) hydrogen bonds : bond 0.03909 ( 1760) hydrogen bonds : angle 4.21619 ( 4861) metal coordination : bond 0.00710 ( 32) metal coordination : angle 5.33030 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 423 time to evaluate : 1.270 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: A 65 LEU cc_start: 0.9394 (mp) cc_final: 0.8897 (pp) REVERT: A 68 GLN cc_start: 0.9037 (mp10) cc_final: 0.8635 (mp10) REVERT: A 76 GLU cc_start: 0.8901 (mp0) cc_final: 0.8678 (mp0) REVERT: A 618 GLU cc_start: 0.8148 (pm20) cc_final: 0.7753 (pm20) REVERT: A 826 ASP cc_start: 0.8702 (m-30) cc_final: 0.8207 (t0) REVERT: A 1078 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8483 (tp-100) REVERT: A 1112 LYS cc_start: 0.9233 (mtpt) cc_final: 0.8671 (mmmm) REVERT: A 1228 TRP cc_start: 0.7026 (m-90) cc_final: 0.6725 (m-90) REVERT: A 1337 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: A 1420 ASP cc_start: 0.8588 (p0) cc_final: 0.8381 (p0) REVERT: A 1454 MET cc_start: 0.8506 (tpt) cc_final: 0.8193 (tpt) REVERT: B 239 GLU cc_start: 0.8766 (pm20) cc_final: 0.7658 (pm20) REVERT: B 241 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8179 (mtp85) REVERT: B 396 ASP cc_start: 0.8765 (m-30) cc_final: 0.8325 (m-30) REVERT: B 510 LYS cc_start: 0.8906 (tppp) cc_final: 0.8269 (tmmt) REVERT: B 687 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 816 GLU cc_start: 0.8748 (mp0) cc_final: 0.8333 (mp0) REVERT: B 868 MET cc_start: 0.8328 (tpp) cc_final: 0.8045 (tpp) REVERT: B 1111 MET cc_start: 0.9060 (mmm) cc_final: 0.8744 (mmm) REVERT: B 1125 ASP cc_start: 0.8943 (t0) cc_final: 0.8414 (t0) REVERT: C 12 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8177 (tm-30) REVERT: F 110 ASP cc_start: 0.9074 (p0) cc_final: 0.8757 (p0) REVERT: F 111 LEU cc_start: 0.9316 (mt) cc_final: 0.9076 (mp) REVERT: F 112 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8810 (tm-30) REVERT: F 127 GLU cc_start: 0.9026 (pm20) cc_final: 0.8751 (pm20) REVERT: H 67 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8204 (OUTLIER) REVERT: H 135 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8229 (pp) REVERT: I 11 ASN cc_start: 0.7773 (t0) cc_final: 0.6926 (t0) REVERT: I 47 GLU cc_start: 0.8234 (tp30) cc_final: 0.7439 (tm-30) REVERT: I 48 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8965 (mm) REVERT: J 27 GLU cc_start: 0.8780 (pp20) cc_final: 0.8369 (pp20) REVERT: K 8 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8330 (mm-30) REVERT: K 24 ASP cc_start: 0.8506 (t0) cc_final: 0.8185 (t0) REVERT: K 36 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8095 (mm-30) REVERT: K 38 GLU cc_start: 0.8467 (mp0) cc_final: 0.7856 (pm20) REVERT: L 40 LEU cc_start: 0.8409 (pp) cc_final: 0.8107 (pt) REVERT: L 44 ASP cc_start: 0.8784 (t0) cc_final: 0.8387 (t0) REVERT: W 808 ARG cc_start: 0.6218 (ptp90) cc_final: 0.5926 (pmm-80) REVERT: G 1 MET cc_start: 0.8150 (tmm) cc_final: 0.7908 (ppp) REVERT: G 25 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7976 (t80) REVERT: G 53 ASN cc_start: 0.8182 (t0) cc_final: 0.7934 (t0) REVERT: G 75 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6776 (ptm160) REVERT: G 114 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7683 (mp) REVERT: G 144 ARG cc_start: 0.4046 (ttp-170) cc_final: 0.3658 (mtt90) REVERT: M 54 MET cc_start: 0.7608 (mmp) cc_final: 0.7326 (mmp) REVERT: M 109 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8260 (tppp) REVERT: M 298 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8336 (ptt-90) REVERT: M 395 ARG cc_start: 0.3382 (mtm110) cc_final: 0.2137 (mtt180) REVERT: M 640 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8463 (tpp) REVERT: M 665 HIS cc_start: 0.4610 (OUTLIER) cc_final: 0.4242 (p-80) REVERT: M 728 LYS cc_start: 0.0373 (mtmt) cc_final: -0.0211 (tmtp) REVERT: M 850 LEU cc_start: 0.5600 (OUTLIER) cc_final: 0.5256 (mp) REVERT: O 358 ILE cc_start: 0.3023 (OUTLIER) cc_final: 0.2150 (mt) REVERT: O 365 TYR cc_start: 0.0061 (OUTLIER) cc_final: -0.0920 (t80) outliers start: 139 outliers final: 104 residues processed: 526 average time/residue: 0.6778 time to fit residues: 435.3959 Evaluate side-chains 529 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 413 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1185 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 298 ARG Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 314 PHE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 599 LEU Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 640 MET Chi-restraints excluded: chain M residue 646 CYS Chi-restraints excluded: chain M residue 665 HIS Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 850 LEU Chi-restraints excluded: chain M residue 929 GLU Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 127 ARG Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 358 ILE Chi-restraints excluded: chain O residue 365 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 479 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 446 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 503 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 165 optimal weight: 0.0870 chunk 176 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS A1110 ASN A1432 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN H 137 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN O 305 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.157005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088606 restraints weight = 78008.049| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.93 r_work: 0.2861 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43770 Z= 0.123 Angle : 0.604 15.725 59589 Z= 0.300 Chirality : 0.042 0.408 6663 Planarity : 0.004 0.058 7380 Dihedral : 13.927 177.770 6738 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 2.69 % Allowed : 26.11 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.12), residues: 5075 helix: 1.70 (0.13), residues: 1766 sheet: 0.26 (0.19), residues: 778 loop : -0.68 (0.13), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 175 TYR 0.027 0.001 TYR M 300 PHE 0.020 0.001 PHE A 219 TRP 0.009 0.001 TRP B 31 HIS 0.004 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00280 (43738) covalent geometry : angle 0.58893 (59544) hydrogen bonds : bond 0.03446 ( 1760) hydrogen bonds : angle 4.12769 ( 4861) metal coordination : bond 0.00513 ( 32) metal coordination : angle 4.84699 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10150 Ramachandran restraints generated. 5075 Oldfield, 0 Emsley, 5075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 435 time to evaluate : 1.178 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: A 65 LEU cc_start: 0.9405 (mp) cc_final: 0.8928 (pp) REVERT: A 68 GLN cc_start: 0.9074 (mp10) cc_final: 0.8719 (mp10) REVERT: A 76 GLU cc_start: 0.8886 (mp0) cc_final: 0.8647 (mp0) REVERT: A 618 GLU cc_start: 0.8105 (pm20) cc_final: 0.7681 (pm20) REVERT: A 826 ASP cc_start: 0.8695 (m-30) cc_final: 0.8196 (t0) REVERT: A 1078 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8500 (tp-100) REVERT: A 1112 LYS cc_start: 0.9274 (mtpt) cc_final: 0.8709 (mmmm) REVERT: A 1228 TRP cc_start: 0.6921 (m-90) cc_final: 0.6563 (m-90) REVERT: A 1312 ASN cc_start: 0.8148 (t0) cc_final: 0.7429 (t0) REVERT: A 1337 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8373 (mp0) REVERT: A 1420 ASP cc_start: 0.8499 (p0) cc_final: 0.8283 (p0) REVERT: A 1454 MET cc_start: 0.8453 (tpt) cc_final: 0.8157 (tpt) REVERT: B 239 GLU cc_start: 0.8732 (pm20) cc_final: 0.7630 (pm20) REVERT: B 241 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8133 (mtp85) REVERT: B 396 ASP cc_start: 0.8722 (m-30) cc_final: 0.8317 (m-30) REVERT: B 510 LYS cc_start: 0.8819 (tppp) cc_final: 0.8189 (tmmt) REVERT: B 687 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8048 (tm-30) REVERT: B 816 GLU cc_start: 0.8757 (mp0) cc_final: 0.8388 (mp0) REVERT: B 868 MET cc_start: 0.8373 (tpp) cc_final: 0.8093 (tpp) REVERT: B 946 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8314 (p0) REVERT: B 1111 MET cc_start: 0.9026 (mmm) cc_final: 0.8683 (mmm) REVERT: B 1120 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8112 (tp30) REVERT: B 1125 ASP cc_start: 0.8932 (t0) cc_final: 0.8318 (t0) REVERT: C 12 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8192 (tm-30) REVERT: F 110 ASP cc_start: 0.9065 (p0) cc_final: 0.8730 (p0) REVERT: F 111 LEU cc_start: 0.9302 (mt) cc_final: 0.9039 (mp) REVERT: F 112 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8780 (tm-30) REVERT: H 135 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8196 (pp) REVERT: I 11 ASN cc_start: 0.7756 (t0) cc_final: 0.6927 (t0) REVERT: I 47 GLU cc_start: 0.8234 (tp30) cc_final: 0.7451 (tm-30) REVERT: I 48 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8924 (mm) REVERT: K 8 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8347 (mm-30) REVERT: K 24 ASP cc_start: 0.8517 (t0) cc_final: 0.8211 (t0) REVERT: K 36 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8063 (mm-30) REVERT: K 38 GLU cc_start: 0.8474 (mp0) cc_final: 0.7872 (pm20) REVERT: L 40 LEU cc_start: 0.8438 (pp) cc_final: 0.8209 (pt) REVERT: L 44 ASP cc_start: 0.8819 (t0) cc_final: 0.8440 (t0) REVERT: W 808 ARG cc_start: 0.6056 (ptp90) cc_final: 0.5790 (pmm-80) REVERT: G 1 MET cc_start: 0.8338 (tmm) cc_final: 0.8106 (ppp) REVERT: G 25 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7982 (t80) REVERT: G 33 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8817 (tm-30) REVERT: G 51 TYR cc_start: 0.8460 (t80) cc_final: 0.7970 (t80) REVERT: G 53 ASN cc_start: 0.8275 (t0) cc_final: 0.8064 (t0) REVERT: G 75 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6762 (ptm160) REVERT: G 114 LEU cc_start: 0.8140 (mm) cc_final: 0.7669 (mp) REVERT: G 144 ARG cc_start: 0.4152 (ttp-170) cc_final: 0.3709 (mtt90) REVERT: M 54 MET cc_start: 0.7802 (mmp) cc_final: 0.7487 (mmp) REVERT: M 109 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8198 (tppp) REVERT: M 258 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: M 395 ARG cc_start: 0.3366 (mtm110) cc_final: 0.1976 (mtt180) REVERT: M 640 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8345 (tpp) REVERT: M 665 HIS cc_start: 0.4392 (OUTLIER) cc_final: 0.3860 (p-80) REVERT: M 728 LYS cc_start: 0.0279 (mtmt) cc_final: -0.0379 (tmtp) REVERT: M 850 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5290 (mp) REVERT: O 358 ILE cc_start: 0.2677 (OUTLIER) cc_final: 0.1581 (mt) REVERT: O 365 TYR cc_start: 0.0133 (OUTLIER) cc_final: -0.0910 (t80) outliers start: 120 outliers final: 89 residues processed: 526 average time/residue: 0.6188 time to fit residues: 399.0190 Evaluate side-chains 527 residues out of total 4529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 425 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1110 ASN Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1337 GLU Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 891 ASP Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1185 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain W residue 819 VAL Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 109 LYS Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 258 GLN Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 299 GLU Chi-restraints excluded: chain M residue 314 PHE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 599 LEU Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain M residue 640 MET Chi-restraints excluded: chain M residue 665 HIS Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 850 LEU Chi-restraints excluded: chain M residue 929 GLU Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 127 ARG Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 298 VAL Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 358 ILE Chi-restraints excluded: chain O residue 365 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 515 random chunks: chunk 370 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 362 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 278 optimal weight: 0.0570 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 490 optimal weight: 10.0000 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS H 137 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 283 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.155786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087079 restraints weight = 78630.808| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.95 r_work: 0.2833 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43770 Z= 0.189 Angle : 0.632 17.023 59589 Z= 0.313 Chirality : 0.043 0.397 6663 Planarity : 0.004 0.059 7380 Dihedral : 13.947 177.997 6738 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 2.62 % Allowed : 26.40 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.12), residues: 5075 helix: 1.62 (0.12), residues: 1778 sheet: 0.25 (0.19), residues: 775 loop : -0.75 (0.13), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B 430 TYR 0.026 0.001 TYR M 300 PHE 0.024 0.001 PHE A 219 TRP 0.012 0.001 TRP M 188 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00447 (43738) covalent geometry : angle 0.61640 (59544) hydrogen bonds : bond 0.03823 ( 1760) hydrogen bonds : angle 4.18379 ( 4861) metal coordination : bond 0.00691 ( 32) metal coordination : angle 5.12657 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18762.50 seconds wall clock time: 318 minutes 29.12 seconds (19109.12 seconds total)