Starting phenix.real_space_refine on Sat Dec 28 02:28:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8e_37352/12_2024/8w8e_37352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8e_37352/12_2024/8w8e_37352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w8e_37352/12_2024/8w8e_37352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8e_37352/12_2024/8w8e_37352.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8e_37352/12_2024/8w8e_37352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8e_37352/12_2024/8w8e_37352.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.008 sd= 0.077 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 98 5.49 5 Mg 1 5.21 5 S 300 5.16 5 C 31918 2.51 5 N 8880 2.21 5 O 9707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 50912 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 11299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 11299 Classifications: {'peptide': 1426} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 70, 'TRANS': 1355} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 9046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 9046 Classifications: {'peptide': 1133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1079} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 997 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1305 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 714 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain breaks: 1 Chain: "P" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 347 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna2p': 4, 'rna3p': 11} Chain: "T" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 910 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "U" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1410 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "V" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4411 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 26, 'TRANS': 523} Chain: "W" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3823 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 23, 'TRANS': 508} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 542 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 243 Chain: "X" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 293 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2880 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain breaks: 5 Chain: "a" Number of atoms: 4096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 506, 4082 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 471} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 506, 4082 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 471} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4163 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 768 SG CYS A 111 147.218 81.333 66.119 1.00 52.15 S ATOM 796 SG CYS A 114 150.633 82.707 64.210 1.00 60.58 S ATOM 464 SG CYS A 71 150.306 88.383 113.004 1.00 41.25 S ATOM 486 SG CYS A 74 148.214 91.635 112.923 1.00 35.32 S ATOM 533 SG CYS A 81 146.434 88.307 113.350 1.00 35.83 S ATOM 19914 SG CYS B1119 144.666 98.907 100.064 1.00 32.24 S ATOM 19936 SG CYS B1122 145.336 97.276 97.168 1.00 35.98 S ATOM 20051 SG CYS B1137 147.432 97.045 100.191 1.00 48.78 S ATOM 21039 SG CYS C 88 108.791 78.894 167.472 1.00 27.25 S ATOM 21052 SG CYS C 90 112.057 77.346 166.347 1.00 37.75 S ATOM 21087 SG CYS C 94 109.835 75.643 168.859 1.00 23.11 S ATOM 21109 SG CYS C 97 108.727 75.682 165.254 1.00 16.65 S ATOM 28353 SG CYS I 17 117.514 22.274 57.167 1.00 39.89 S ATOM 28377 SG CYS I 20 120.618 23.464 59.097 1.00 41.99 S ATOM 28538 SG CYS I 39 118.848 26.035 57.212 1.00 38.99 S ATOM 28563 SG CYS I 42 120.471 22.994 55.314 1.00 43.23 S ATOM 28915 SG CYS I 86 80.723 20.338 81.842 1.00 32.07 S ATOM 28939 SG CYS I 89 80.788 17.397 83.597 1.00 31.64 S ATOM 29178 SG CYS I 119 84.146 17.945 83.742 1.00 38.63 S ATOM 30764 SG CYS L 22 134.026 39.938 146.482 1.00 35.66 S ATOM 30881 SG CYS L 36 136.943 41.865 147.110 1.00 37.97 S ATOM 43103 SG CYS Y 16 187.921 47.216 87.834 1.00 81.24 S ATOM 43125 SG CYS Y 19 185.775 45.510 84.952 1.00 84.47 S ATOM 43237 SG CYS Y 33 187.806 43.147 86.705 1.00 73.71 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N APRO a 7 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO a 7 " occ=0.50 residue: pdb=" N AGLY a 62 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY a 62 " occ=0.50 residue: pdb=" N GLU a 195 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU a 195 " occ=0.50 residue: pdb=" N ASP a 196 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP a 196 " occ=0.50 Time building chain proxies: 23.19, per 1000 atoms: 0.46 Number of scatterers: 50912 At special positions: 0 Unit cell: (214.774, 158.746, 208.104, 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 300 16.00 P 98 15.00 Mg 1 11.99 O 9707 8.00 N 8880 7.00 C 31918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.67 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " Number of angles added : 15 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11664 Finding SS restraints... Secondary structure from input PDB file: 239 helices and 60 sheets defined 44.1% alpha, 14.6% beta 26 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 13.77 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.546A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 297 removed outlier: 3.787A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.395A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.345A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.553A pdb=" N ASP A 437 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 439' Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.970A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.923A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 removed outlier: 3.568A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 757 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.541A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.503A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.072A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.853A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 removed outlier: 3.569A pdb=" N ALA A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 4.095A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1117 removed outlier: 4.169A pdb=" N ASN A1116 " --> pdb=" O SER A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 3.956A pdb=" N GLU A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1191 through 1197 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.615A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 4.003A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.900A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.753A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.512A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1461 Processing helix chain 'A' and resid 1478 through 1482 Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.206A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.417A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.762A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 4.222A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 335 through 346 Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.797A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 450 removed outlier: 4.241A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 583 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.570A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.700A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.603A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.515A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.061A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.776A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.812A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.764A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.854A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.530A pdb=" N GLN D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 16 through 20' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.546A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR D 28 " --> pdb=" O GLU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.593A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.890A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.525A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 removed outlier: 4.323A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.570A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.755A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.874A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.150A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.704A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.808A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.865A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 5.753A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 removed outlier: 3.539A pdb=" N THR K 92 " --> pdb=" O THR K 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 18 Processing helix chain 'U' and resid 34 through 42 Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 64 through 71 removed outlier: 3.767A pdb=" N MET U 71 " --> pdb=" O THR U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 84 removed outlier: 3.570A pdb=" N LEU U 75 " --> pdb=" O MET U 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU U 84 " --> pdb=" O GLN U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 98 Processing helix chain 'U' and resid 114 through 131 Processing helix chain 'U' and resid 138 through 143 removed outlier: 3.694A pdb=" N GLN U 142 " --> pdb=" O LEU U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 154 Processing helix chain 'U' and resid 169 through 187 removed outlier: 4.069A pdb=" N THR U 173 " --> pdb=" O PRO U 169 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 22 Processing helix chain 'V' and resid 26 through 38 Processing helix chain 'V' and resid 41 through 53 removed outlier: 3.706A pdb=" N GLN V 45 " --> pdb=" O LEU V 41 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER V 46 " --> pdb=" O PRO V 42 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA V 47 " --> pdb=" O SER V 43 " (cutoff:3.500A) Proline residue: V 49 - end of helix Processing helix chain 'V' and resid 59 through 83 Processing helix chain 'V' and resid 85 through 101 Processing helix chain 'V' and resid 102 through 104 No H-bonds generated for 'chain 'V' and resid 102 through 104' Processing helix chain 'V' and resid 109 through 119 Processing helix chain 'V' and resid 124 through 134 removed outlier: 3.523A pdb=" N ASP V 134 " --> pdb=" O LEU V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 141 Processing helix chain 'V' and resid 142 through 151 Processing helix chain 'V' and resid 153 through 177 Proline residue: V 163 - end of helix Processing helix chain 'V' and resid 191 through 196 Processing helix chain 'V' and resid 198 through 209 Processing helix chain 'V' and resid 211 through 230 Processing helix chain 'V' and resid 232 through 248 Processing helix chain 'V' and resid 250 through 255 Processing helix chain 'V' and resid 259 through 273 Processing helix chain 'V' and resid 276 through 289 Processing helix chain 'V' and resid 295 through 306 removed outlier: 3.756A pdb=" N GLY V 299 " --> pdb=" O GLU V 295 " (cutoff:3.500A) Processing helix chain 'V' and resid 307 through 329 Processing helix chain 'V' and resid 331 through 334 Processing helix chain 'V' and resid 335 through 350 Processing helix chain 'V' and resid 350 through 358 Processing helix chain 'V' and resid 366 through 392 removed outlier: 3.879A pdb=" N ILE V 370 " --> pdb=" O GLU V 366 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU V 374 " --> pdb=" O ILE V 370 " (cutoff:3.500A) Proline residue: V 375 - end of helix removed outlier: 3.535A pdb=" N LYS V 392 " --> pdb=" O ASN V 388 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 398 removed outlier: 5.943A pdb=" N GLU V 396 " --> pdb=" O LEU V 393 " (cutoff:3.500A) Processing helix chain 'V' and resid 408 through 418 Processing helix chain 'V' and resid 418 through 435 Processing helix chain 'V' and resid 437 through 445 Processing helix chain 'V' and resid 446 through 449 removed outlier: 3.531A pdb=" N VAL V 449 " --> pdb=" O PRO V 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 446 through 449' Processing helix chain 'V' and resid 451 through 457 removed outlier: 5.913A pdb=" N ALA V 456 " --> pdb=" O GLY V 453 " (cutoff:3.500A) Processing helix chain 'V' and resid 458 through 470 Processing helix chain 'V' and resid 471 through 477 removed outlier: 5.354A pdb=" N ASP V 474 " --> pdb=" O LEU V 471 " (cutoff:3.500A) Processing helix chain 'V' and resid 478 through 489 Processing helix chain 'V' and resid 489 through 494 removed outlier: 3.992A pdb=" N ALA V 493 " --> pdb=" O PHE V 489 " (cutoff:3.500A) Processing helix chain 'V' and resid 497 through 512 Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 527 Processing helix chain 'V' and resid 534 through 554 Processing helix chain 'W' and resid 58 through 60 No H-bonds generated for 'chain 'W' and resid 58 through 60' Processing helix chain 'W' and resid 61 through 68 removed outlier: 3.744A pdb=" N LYS W 67 " --> pdb=" O PHE W 63 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG W 68 " --> pdb=" O ASN W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 84 Processing helix chain 'W' and resid 90 through 103 removed outlier: 3.950A pdb=" N GLU W 99 " --> pdb=" O ASN W 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP W 100 " --> pdb=" O LEU W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 109 through 128 removed outlier: 3.825A pdb=" N GLU W 113 " --> pdb=" O VAL W 109 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS W 126 " --> pdb=" O LEU W 122 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE W 127 " --> pdb=" O LEU W 123 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 139 Processing helix chain 'W' and resid 142 through 152 removed outlier: 4.111A pdb=" N LEU W 146 " --> pdb=" O THR W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 164 removed outlier: 3.881A pdb=" N GLU W 164 " --> pdb=" O TYR W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 182 Processing helix chain 'W' and resid 197 through 216 removed outlier: 3.793A pdb=" N ARG W 203 " --> pdb=" O GLU W 199 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 223 removed outlier: 4.092A pdb=" N LYS W 222 " --> pdb=" O GLU W 218 " (cutoff:3.500A) Processing helix chain 'W' and resid 223 through 232 removed outlier: 4.833A pdb=" N MET W 230 " --> pdb=" O GLU W 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL W 231 " --> pdb=" O PHE W 227 " (cutoff:3.500A) Processing helix chain 'W' and resid 234 through 249 Processing helix chain 'W' and resid 254 through 273 removed outlier: 4.323A pdb=" N VAL W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 284 Processing helix chain 'W' and resid 285 through 288 Processing helix chain 'W' and resid 289 through 303 removed outlier: 3.589A pdb=" N CYS W 293 " --> pdb=" O TYR W 289 " (cutoff:3.500A) Processing helix chain 'W' and resid 306 through 317 removed outlier: 3.543A pdb=" N MET W 316 " --> pdb=" O VAL W 312 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 328 Processing helix chain 'W' and resid 330 through 343 removed outlier: 3.886A pdb=" N LYS W 343 " --> pdb=" O GLN W 339 " (cutoff:3.500A) Processing helix chain 'W' and resid 352 through 366 removed outlier: 3.846A pdb=" N VAL W 366 " --> pdb=" O TYR W 362 " (cutoff:3.500A) Processing helix chain 'W' and resid 382 through 400 removed outlier: 3.944A pdb=" N GLU W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 410 through 418 Processing helix chain 'W' and resid 420 through 436 Processing helix chain 'W' and resid 449 through 462 Processing helix chain 'W' and resid 465 through 479 Processing helix chain 'W' and resid 485 through 506 Processing helix chain 'W' and resid 509 through 522 Processing helix chain 'W' and resid 526 through 539 removed outlier: 3.579A pdb=" N ILE W 530 " --> pdb=" O ASP W 526 " (cutoff:3.500A) Processing helix chain 'W' and resid 546 through 559 Proline residue: W 555 - end of helix Processing helix chain 'W' and resid 562 through 566 removed outlier: 3.606A pdb=" N THR W 565 " --> pdb=" O ILE W 562 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE W 566 " --> pdb=" O ALA W 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 562 through 566' Processing helix chain 'W' and resid 575 through 586 Processing helix chain 'X' and resid 9 through 37 Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 removed outlier: 3.506A pdb=" N VAL Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 188 through 203 removed outlier: 3.562A pdb=" N THR Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 231 through 239 removed outlier: 3.616A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 249 removed outlier: 3.589A pdb=" N LEU Z 245 " --> pdb=" O VAL Z 242 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU Z 247 " --> pdb=" O ASN Z 244 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.545A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'a' and resid 32 through 36 Processing helix chain 'a' and resid 40 through 44 removed outlier: 4.029A pdb=" N ARG a 44 " --> pdb=" O GLU a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 57 Processing helix chain 'a' and resid 75 through 81 removed outlier: 4.050A pdb=" N ILE a 79 " --> pdb=" O ASP a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 111 Processing helix chain 'a' and resid 130 through 145 Processing helix chain 'a' and resid 148 through 160 Processing helix chain 'a' and resid 166 through 178 Processing helix chain 'a' and resid 179 through 183 Processing helix chain 'a' and resid 246 through 262 removed outlier: 3.808A pdb=" N GLY a 251 " --> pdb=" O GLN a 247 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU a 252 " --> pdb=" O PRO a 248 " (cutoff:3.500A) Processing helix chain 'a' and resid 280 through 285 Processing helix chain 'a' and resid 371 through 375 Processing helix chain 'a' and resid 376 through 388 Processing helix chain 'a' and resid 388 through 396 removed outlier: 3.749A pdb=" N LYS a 395 " --> pdb=" O PRO a 391 " (cutoff:3.500A) Processing helix chain 'a' and resid 417 through 425 removed outlier: 4.141A pdb=" N LYS a 423 " --> pdb=" O CYS a 419 " (cutoff:3.500A) Processing helix chain 'a' and resid 506 through 510 Processing helix chain 'a' and resid 538 through 551 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.530A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.683A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 362 through 369 removed outlier: 8.288A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.745A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.700A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.577A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.205A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.205A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.936A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB7, first strand: chain 'A' and resid 1139 through 1140 removed outlier: 3.685A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1243 through 1246 removed outlier: 3.929A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1308 through 1310 Processing sheet with id=AC1, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC2, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.947A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.505A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.367A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 205 through 208 removed outlier: 4.293A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD1, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.169A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.757A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.757A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD5, first strand: chain 'B' and resid 827 through 829 removed outlier: 7.358A pdb=" N GLN B 838 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.604A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD8, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.913A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.394A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE3, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.737A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.737A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 102 through 105 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.133A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.593A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AE9, first strand: chain 'H' and resid 139 through 142 removed outlier: 3.789A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG H 27 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF5, first strand: chain 'Y' and resid 83 through 90 removed outlier: 7.135A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 278 through 280 removed outlier: 6.789A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 352 through 355 Processing sheet with id=AF8, first strand: chain 'Z' and resid 453 through 454 Processing sheet with id=AF9, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.348A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.962A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 24 through 28 removed outlier: 3.941A pdb=" N CYS a 126 " --> pdb=" O LEU a 27 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 241 through 243 removed outlier: 4.076A pdb=" N VAL a 310 " --> pdb=" O VAL a 322 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU a 341 " --> pdb=" O ILE a 364 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE a 364 " --> pdb=" O LEU a 341 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP a 343 " --> pdb=" O TYR a 362 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 271 through 274 removed outlier: 4.087A pdb=" N VAL a 274 " --> pdb=" O CYS a 453 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASP a 455 " --> pdb=" O VAL a 274 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 470 through 474 removed outlier: 6.696A pdb=" N VAL a 491 " --> pdb=" O PRO a 497 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 515 through 520 removed outlier: 6.594A pdb=" N GLU a 516 " --> pdb=" O MET a 527 " (cutoff:3.500A) 2230 hydrogen bonds defined for protein. 6267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 23.87 Time building geometry restraints manager: 11.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8406 1.31 - 1.44: 13464 1.44 - 1.56: 29551 1.56 - 1.69: 192 1.69 - 1.82: 470 Bond restraints: 52083 Sorted by residual: bond pdb=" CA ARG A 734 " pdb=" C ARG A 734 " ideal model delta sigma weight residual 1.522 1.445 0.078 1.36e-02 5.41e+03 3.27e+01 bond pdb=" C PRO A 414 " pdb=" O PRO A 414 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.30e-02 5.92e+03 1.66e+01 bond pdb=" N LYS A 910 " pdb=" CA LYS A 910 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.41e-02 5.03e+03 8.56e+00 bond pdb=" N VAL W 109 " pdb=" CA VAL W 109 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.45e+00 bond pdb=" N PHE a 535 " pdb=" CA PHE a 535 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.41e-02 5.03e+03 8.21e+00 ... (remaining 52078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 70503 3.26 - 6.53: 295 6.53 - 9.79: 24 9.79 - 13.06: 8 13.06 - 16.32: 4 Bond angle restraints: 70834 Sorted by residual: angle pdb=" C GLN B 631 " pdb=" N LYS B 632 " pdb=" CA LYS B 632 " ideal model delta sigma weight residual 122.93 106.61 16.32 1.45e+00 4.76e-01 1.27e+02 angle pdb=" CA PHE a 535 " pdb=" CB PHE a 535 " pdb=" CG PHE a 535 " ideal model delta sigma weight residual 113.80 124.71 -10.91 1.00e+00 1.00e+00 1.19e+02 angle pdb=" C GLY A 415 " pdb=" N ALA A 416 " pdb=" CA ALA A 416 " ideal model delta sigma weight residual 122.81 137.04 -14.23 1.68e+00 3.54e-01 7.17e+01 angle pdb=" C PHE a 535 " pdb=" CA PHE a 535 " pdb=" CB PHE a 535 " ideal model delta sigma weight residual 110.17 126.08 -15.91 1.97e+00 2.58e-01 6.52e+01 angle pdb=" C PRO a 536 " pdb=" CA PRO a 536 " pdb=" CB PRO a 536 " ideal model delta sigma weight residual 111.56 99.14 12.42 1.65e+00 3.67e-01 5.66e+01 ... (remaining 70829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 30675 35.65 - 71.31: 917 71.31 - 106.96: 36 106.96 - 142.61: 5 142.61 - 178.27: 2 Dihedral angle restraints: 31635 sinusoidal: 13635 harmonic: 18000 Sorted by residual: dihedral pdb=" C PHE a 535 " pdb=" N PHE a 535 " pdb=" CA PHE a 535 " pdb=" CB PHE a 535 " ideal model delta harmonic sigma weight residual -122.60 -144.98 22.38 0 2.50e+00 1.60e-01 8.01e+01 dihedral pdb=" N PHE a 535 " pdb=" C PHE a 535 " pdb=" CA PHE a 535 " pdb=" CB PHE a 535 " ideal model delta harmonic sigma weight residual 122.80 139.16 -16.36 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" C8 GTP P 101 " pdb=" C1' GTP P 101 " pdb=" N9 GTP P 101 " pdb=" O4' GTP P 101 " ideal model delta sinusoidal sigma weight residual 104.59 -33.92 138.51 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 31632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 7948 0.145 - 0.290: 31 0.290 - 0.435: 0 0.435 - 0.580: 0 0.580 - 0.724: 1 Chirality restraints: 7980 Sorted by residual: chirality pdb=" CA PHE a 535 " pdb=" N PHE a 535 " pdb=" C PHE a 535 " pdb=" CB PHE a 535 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA PRO W 108 " pdb=" N PRO W 108 " pdb=" C PRO W 108 " pdb=" CB PRO W 108 " both_signs ideal model delta sigma weight residual False 2.72 3.00 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA GLU B 629 " pdb=" N GLU B 629 " pdb=" C GLU B 629 " pdb=" CB GLU B 629 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 7977 not shown) Planarity restraints: 8828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 415 " 0.021 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C GLY A 415 " -0.075 2.00e-02 2.50e+03 pdb=" O GLY A 415 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 416 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 631 " -0.020 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLN B 631 " 0.072 2.00e-02 2.50e+03 pdb=" O GLN B 631 " -0.028 2.00e-02 2.50e+03 pdb=" N LYS B 632 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY W 105 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C GLY W 105 " 0.056 2.00e-02 2.50e+03 pdb=" O GLY W 105 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL W 106 " -0.018 2.00e-02 2.50e+03 ... (remaining 8825 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 172 2.46 - 3.07: 33116 3.07 - 3.68: 78531 3.68 - 4.29: 116649 4.29 - 4.90: 189464 Nonbonded interactions: 417932 Sorted by model distance: nonbonded pdb=" O3' U P 46 " pdb="MG MG A2001 " model vdw 1.853 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 1.908 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.064 2.170 nonbonded pdb=" ND2 ASN a 52 " pdb=" O ASP a 511 " model vdw 2.087 3.120 nonbonded pdb=" N2 DG N 43 " pdb=" N3 DC T 6 " model vdw 2.110 2.560 ... (remaining 417927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 1.530 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 110.410 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 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 : 0.003 0.078 52083 Z= 0.166 Angle : 0.620 16.324 70834 Z= 0.336 Chirality : 0.044 0.724 7980 Planarity : 0.004 0.061 8828 Dihedral : 14.489 178.268 19971 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.86 % Favored : 93.88 % Rotamer: Outliers : 3.65 % Allowed : 5.52 % Favored : 90.82 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 6120 helix: 0.49 (0.11), residues: 2430 sheet: -1.49 (0.18), residues: 746 loop : -1.61 (0.11), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1192 HIS 0.007 0.001 HIS B 460 PHE 0.033 0.001 PHE a 535 TYR 0.038 0.001 TYR a 289 ARG 0.013 0.000 ARG a 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1396 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 1203 time to evaluate : 4.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6345 (m) REVERT: A 296 ASN cc_start: 0.6478 (p0) cc_final: 0.5707 (p0) REVERT: A 317 MET cc_start: 0.8123 (tmm) cc_final: 0.7862 (tmm) REVERT: A 318 VAL cc_start: 0.8451 (t) cc_final: 0.8251 (t) REVERT: A 841 MET cc_start: 0.7421 (mtt) cc_final: 0.7117 (mtt) REVERT: A 1190 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: A 1191 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.4400 (tp30) REVERT: A 1341 VAL cc_start: 0.8236 (p) cc_final: 0.7915 (p) REVERT: A 1405 MET cc_start: 0.7335 (mtp) cc_final: 0.7079 (ttp) REVERT: A 1440 MET cc_start: 0.8030 (mmm) cc_final: 0.7457 (mmt) REVERT: A 1451 MET cc_start: 0.7055 (mtp) cc_final: 0.6379 (mtm) REVERT: A 1460 LEU cc_start: 0.8503 (mm) cc_final: 0.7798 (mp) REVERT: B 117 ASN cc_start: 0.7675 (m-40) cc_final: 0.7072 (m-40) REVERT: B 508 MET cc_start: 0.7350 (mpt) cc_final: 0.7125 (mpp) REVERT: B 584 MET cc_start: 0.7030 (mmm) cc_final: 0.6499 (mmm) REVERT: B 1041 ILE cc_start: 0.9228 (mm) cc_final: 0.8991 (mt) REVERT: B 1052 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8104 (pttp) REVERT: B 1159 PHE cc_start: 0.8241 (m-10) cc_final: 0.7989 (m-10) REVERT: C 44 ILE cc_start: 0.8597 (pt) cc_final: 0.8366 (pt) REVERT: C 161 LEU cc_start: 0.7353 (pp) cc_final: 0.7116 (pp) REVERT: E 34 ASP cc_start: 0.5443 (p0) cc_final: 0.5172 (p0) REVERT: E 58 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7740 (pp) REVERT: F 60 TYR cc_start: 0.8571 (m-80) cc_final: 0.8191 (m-80) REVERT: F 91 LEU cc_start: 0.7281 (mt) cc_final: 0.6736 (mt) REVERT: F 102 ILE cc_start: 0.8397 (mt) cc_final: 0.8100 (tt) REVERT: F 123 LEU cc_start: 0.8385 (mt) cc_final: 0.8166 (mt) REVERT: G 70 VAL cc_start: 0.7976 (t) cc_final: 0.7698 (p) REVERT: G 157 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7140 (mm) REVERT: J 21 TYR cc_start: 0.8640 (t80) cc_final: 0.8432 (t80) REVERT: J 48 MET cc_start: 0.8253 (mmm) cc_final: 0.7533 (mmm) REVERT: K 58 PHE cc_start: 0.8127 (t80) cc_final: 0.7914 (t80) REVERT: K 69 HIS cc_start: 0.7388 (m-70) cc_final: 0.7100 (m90) REVERT: V 410 SER cc_start: 0.6361 (OUTLIER) cc_final: 0.6085 (p) REVERT: W 541 ILE cc_start: 0.2507 (OUTLIER) cc_final: 0.1615 (pp) REVERT: a 61 MET cc_start: -0.2261 (OUTLIER) cc_final: -0.2914 (tpp) REVERT: a 287 LYS cc_start: -0.1579 (OUTLIER) cc_final: -0.1913 (ptmt) REVERT: a 396 MET cc_start: -0.1855 (mtp) cc_final: -0.2779 (mtt) outliers start: 193 outliers final: 42 residues processed: 1366 average time/residue: 0.5831 time to fit residues: 1306.5012 Evaluate side-chains 637 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 585 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 1052 LYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 382 VAL Chi-restraints excluded: chain V residue 410 SER Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 541 ILE Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 194 PHE Chi-restraints excluded: chain a residue 276 MET Chi-restraints excluded: chain a residue 287 LYS Chi-restraints excluded: chain a residue 322 VAL Chi-restraints excluded: chain a residue 381 LEU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 422 ARG Chi-restraints excluded: chain a residue 467 VAL Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 514 ILE Chi-restraints excluded: chain a residue 515 ILE Chi-restraints excluded: chain a residue 528 ARG Chi-restraints excluded: chain a residue 530 ARG Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 521 optimal weight: 50.0000 chunk 467 optimal weight: 20.0000 chunk 259 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 315 optimal weight: 0.0770 chunk 249 optimal weight: 6.9990 chunk 483 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 359 optimal weight: 2.9990 chunk 560 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 272 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN A 387 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 507 GLN A 576 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 654 HIS A 662 HIS A 780 ASN A 809 HIS A 905 ASN A 989 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1105 ASN A1129 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN A1244 ASN A1248 ASN A1332 GLN A1457 ASN B 111 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN B 500 GLN B 518 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 HIS B 639 HIS B 649 ASN B 650 ASN B 699 HIS B 741 HIS B 749 HIS B 980 HIS B 986 GLN B1003 ASN B1009 GLN B1021 HIS B1053 HIS B1094 GLN B1129 ASN C 55 ASN C 111 GLN C 232 ASN D 19 GLN D 93 HIS D 135 GLN E 95 GLN E 116 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN H 76 ASN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 HIS V 119 HIS W 223 ASN W 250 GLN ** W 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 354 HIS W 394 HIS W 401 ASN W 502 HIS Y 12 HIS Y 41 GLN a 43 ASN ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN a 158 GLN a 243 GLN a 272 GLN ** a 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 512 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 52083 Z= 0.357 Angle : 0.756 12.799 70834 Z= 0.390 Chirality : 0.046 0.272 7980 Planarity : 0.005 0.079 8828 Dihedral : 15.222 179.886 7897 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.41 % Favored : 94.44 % Rotamer: Outliers : 4.01 % Allowed : 12.96 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.11), residues: 6120 helix: 0.77 (0.11), residues: 2453 sheet: -1.43 (0.18), residues: 743 loop : -1.36 (0.11), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 459 HIS 0.012 0.002 HIS A 449 PHE 0.036 0.002 PHE a 535 TYR 0.026 0.002 TYR a 362 ARG 0.009 0.001 ARG a 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 573 time to evaluate : 4.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.8397 (tmm) cc_final: 0.7817 (tmm) REVERT: A 318 VAL cc_start: 0.8750 (t) cc_final: 0.8080 (t) REVERT: A 520 MET cc_start: 0.8265 (mmp) cc_final: 0.7971 (mmp) REVERT: A 962 ASP cc_start: 0.7396 (m-30) cc_final: 0.7141 (m-30) REVERT: A 1190 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6170 (tt0) REVERT: A 1451 MET cc_start: 0.7415 (mtp) cc_final: 0.7031 (mtm) REVERT: A 1460 LEU cc_start: 0.8584 (mm) cc_final: 0.8055 (mp) REVERT: B 584 MET cc_start: 0.6900 (mmm) cc_final: 0.6559 (mmm) REVERT: B 1041 ILE cc_start: 0.9311 (mm) cc_final: 0.9073 (mm) REVERT: B 1054 MET cc_start: 0.8456 (mmt) cc_final: 0.7936 (mmt) REVERT: D 80 ILE cc_start: 0.6899 (mm) cc_final: 0.6114 (mm) REVERT: E 58 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8078 (pp) REVERT: E 208 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7704 (tt) REVERT: F 82 GLU cc_start: 0.6485 (tp30) cc_final: 0.6082 (tp30) REVERT: F 94 MET cc_start: 0.7385 (tpp) cc_final: 0.7145 (tpt) REVERT: F 102 ILE cc_start: 0.8706 (mt) cc_final: 0.8418 (tt) REVERT: H 116 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.8820 (m) REVERT: J 48 MET cc_start: 0.8855 (mmm) cc_final: 0.8165 (mmm) REVERT: K 56 VAL cc_start: 0.8627 (t) cc_final: 0.8258 (m) REVERT: U 143 TYR cc_start: 0.5082 (m-80) cc_final: 0.4736 (m-10) REVERT: V 376 MET cc_start: 0.7193 (ptm) cc_final: 0.6541 (ptm) REVERT: V 420 MET cc_start: 0.7090 (mmm) cc_final: 0.6685 (mmt) REVERT: Z 474 MET cc_start: 0.4907 (mpp) cc_final: 0.4633 (mmm) REVERT: a 61 MET cc_start: -0.2650 (OUTLIER) cc_final: -0.3525 (tpt) REVERT: a 396 MET cc_start: -0.2142 (mtp) cc_final: -0.2706 (mtt) outliers start: 212 outliers final: 119 residues processed: 745 average time/residue: 0.5145 time to fit residues: 639.4233 Evaluate side-chains 576 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 452 time to evaluate : 4.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1190 GLN Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 114 MET Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 367 VAL Chi-restraints excluded: chain V residue 382 VAL Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 233 HIS Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 414 LEU Chi-restraints excluded: chain W residue 422 VAL Chi-restraints excluded: chain Y residue 6 VAL Chi-restraints excluded: chain Z residue 278 TRP Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 276 MET Chi-restraints excluded: chain a residue 351 VAL Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 422 ARG Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 510 TYR Chi-restraints excluded: chain a residue 514 ILE Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 311 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 chunk 466 optimal weight: 0.0070 chunk 381 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 561 optimal weight: 8.9990 chunk 606 optimal weight: 30.0000 chunk 499 optimal weight: 7.9990 chunk 556 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 450 optimal weight: 10.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 330 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 HIS A1310 HIS A1332 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS K 69 HIS ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 266 GLN ** W 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 352 HIS ** W 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 393 HIS ** a 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 52083 Z= 0.200 Angle : 0.666 12.429 70834 Z= 0.339 Chirality : 0.044 0.258 7980 Planarity : 0.004 0.062 8828 Dihedral : 14.872 178.679 7840 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 3.09 % Allowed : 14.25 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 6120 helix: 0.95 (0.11), residues: 2453 sheet: -1.26 (0.18), residues: 745 loop : -1.22 (0.12), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1192 HIS 0.007 0.001 HIS G 4 PHE 0.040 0.001 PHE E 73 TYR 0.021 0.001 TYR a 539 ARG 0.008 0.000 ARG a 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 525 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7474 (pptt) REVERT: A 520 MET cc_start: 0.8172 (mmp) cc_final: 0.7905 (mmp) REVERT: A 769 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6947 (mtp) REVERT: A 1191 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6633 (pm20) REVERT: A 1293 LEU cc_start: 0.7475 (mm) cc_final: 0.7220 (mm) REVERT: A 1460 LEU cc_start: 0.8749 (mm) cc_final: 0.8400 (mm) REVERT: B 356 PHE cc_start: 0.6431 (m-10) cc_final: 0.6195 (m-10) REVERT: B 416 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7433 (tpp80) REVERT: B 854 ILE cc_start: 0.9329 (mm) cc_final: 0.9023 (mt) REVERT: B 1041 ILE cc_start: 0.9221 (mm) cc_final: 0.8982 (mm) REVERT: B 1054 MET cc_start: 0.8478 (mmt) cc_final: 0.8223 (mmt) REVERT: B 1172 MET cc_start: 0.8099 (mpp) cc_final: 0.7451 (mpp) REVERT: E 58 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8091 (pp) REVERT: F 60 TYR cc_start: 0.8681 (m-80) cc_final: 0.8411 (m-80) REVERT: F 61 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6307 (mt-10) REVERT: F 102 ILE cc_start: 0.8727 (mt) cc_final: 0.8319 (tt) REVERT: J 48 MET cc_start: 0.8811 (mmm) cc_final: 0.8291 (mmm) REVERT: K 38 GLU cc_start: 0.7497 (tp30) cc_final: 0.7205 (tp30) REVERT: K 85 GLU cc_start: 0.6921 (tp30) cc_final: 0.6629 (tp30) REVERT: U 143 TYR cc_start: 0.5042 (m-80) cc_final: 0.4747 (m-10) REVERT: V 376 MET cc_start: 0.7276 (ptm) cc_final: 0.6803 (ptm) REVERT: V 420 MET cc_start: 0.7025 (mmm) cc_final: 0.6547 (mmt) REVERT: W 439 ARG cc_start: 0.1738 (mmm160) cc_final: 0.0899 (mmm160) REVERT: Z 474 MET cc_start: 0.4457 (mpp) cc_final: 0.3925 (mmm) REVERT: a 61 MET cc_start: -0.2667 (OUTLIER) cc_final: -0.3507 (tpt) REVERT: a 301 MET cc_start: 0.1386 (tpt) cc_final: 0.1143 (tpt) REVERT: a 396 MET cc_start: -0.2078 (mtp) cc_final: -0.3220 (mtt) outliers start: 163 outliers final: 91 residues processed: 657 average time/residue: 0.4883 time to fit residues: 543.7337 Evaluate side-chains 546 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 449 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 114 MET Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 367 VAL Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 233 HIS Chi-restraints excluded: chain W residue 266 GLN Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Z residue 278 TRP Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain a residue 61 MET Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 351 VAL Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 422 ARG Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 514 ILE Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 554 optimal weight: 40.0000 chunk 422 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 267 optimal weight: 7.9990 chunk 376 optimal weight: 0.7980 chunk 563 optimal weight: 0.5980 chunk 596 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 533 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN E 35 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 279 GLN ** a 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 52083 Z= 0.273 Angle : 0.663 12.413 70834 Z= 0.339 Chirality : 0.044 0.229 7980 Planarity : 0.004 0.058 8828 Dihedral : 14.667 179.499 7826 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.52 % Rotamer: Outliers : 3.58 % Allowed : 14.63 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 6120 helix: 1.10 (0.11), residues: 2452 sheet: -1.24 (0.18), residues: 748 loop : -1.09 (0.12), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1192 HIS 0.012 0.001 HIS A 839 PHE 0.040 0.002 PHE E 73 TYR 0.024 0.002 TYR a 539 ARG 0.014 0.000 ARG U 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 453 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8251 (mmt) cc_final: 0.7883 (mmt) REVERT: A 769 MET cc_start: 0.7105 (mtp) cc_final: 0.6816 (mtp) REVERT: A 865 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 1102 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7306 (tmm) REVERT: A 1158 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7739 (tm) REVERT: A 1191 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6669 (pm20) REVERT: A 1460 LEU cc_start: 0.8566 (mm) cc_final: 0.8175 (mp) REVERT: B 928 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8728 (pt) REVERT: B 1041 ILE cc_start: 0.9244 (mm) cc_final: 0.9007 (mm) REVERT: B 1054 MET cc_start: 0.8484 (mmt) cc_final: 0.8189 (mmt) REVERT: B 1172 MET cc_start: 0.8269 (mpp) cc_final: 0.7654 (mpp) REVERT: C 263 LEU cc_start: 0.8730 (tp) cc_final: 0.8525 (tt) REVERT: E 58 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (pp) REVERT: F 60 TYR cc_start: 0.8822 (m-80) cc_final: 0.8540 (m-80) REVERT: F 102 ILE cc_start: 0.8760 (mt) cc_final: 0.8462 (tt) REVERT: G 164 MET cc_start: 0.6760 (mmt) cc_final: 0.6317 (mmt) REVERT: J 48 MET cc_start: 0.8926 (mmm) cc_final: 0.8246 (mmm) REVERT: K 85 GLU cc_start: 0.7021 (tp30) cc_final: 0.6679 (tp30) REVERT: U 31 SER cc_start: 0.5258 (OUTLIER) cc_final: 0.4227 (p) REVERT: V 420 MET cc_start: 0.7073 (mmm) cc_final: 0.6723 (mmt) REVERT: W 245 MET cc_start: 0.1367 (tmm) cc_final: 0.0446 (mtm) REVERT: W 439 ARG cc_start: 0.1848 (mmm160) cc_final: 0.1279 (mmm160) REVERT: a 61 MET cc_start: -0.2516 (ttt) cc_final: -0.3493 (tpt) REVERT: a 396 MET cc_start: -0.2080 (mtp) cc_final: -0.2650 (mtt) outliers start: 189 outliers final: 116 residues processed: 608 average time/residue: 0.4982 time to fit residues: 515.0044 Evaluate side-chains 533 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 410 time to evaluate : 4.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 367 VAL Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 233 HIS Chi-restraints excluded: chain W residue 285 THR Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 375 ARG Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 414 LEU Chi-restraints excluded: chain W residue 422 VAL Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 TRP Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 193 CYS Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 351 VAL Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 514 ILE Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 496 optimal weight: 20.0000 chunk 338 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 444 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 508 optimal weight: 10.0000 chunk 412 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 chunk 304 optimal weight: 1.9990 chunk 535 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN A 403 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN E 210 GLN G 4 HIS G 9 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 266 GLN W 270 GLN W 306 ASN ** W 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN ** a 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 52083 Z= 0.296 Angle : 0.665 12.854 70834 Z= 0.339 Chirality : 0.044 0.223 7980 Planarity : 0.004 0.057 8828 Dihedral : 14.553 179.505 7817 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 3.46 % Allowed : 14.72 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 6120 helix: 1.21 (0.11), residues: 2453 sheet: -1.24 (0.18), residues: 754 loop : -0.98 (0.12), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Z 278 HIS 0.008 0.001 HIS A 839 PHE 0.036 0.002 PHE E 73 TYR 0.027 0.002 TYR V 428 ARG 0.007 0.000 ARG U 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 447 time to evaluate : 4.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LEU cc_start: 0.8534 (mt) cc_final: 0.8289 (mt) REVERT: A 499 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7749 (t0) REVERT: A 860 ILE cc_start: 0.9424 (tt) cc_final: 0.9217 (tt) REVERT: A 868 MET cc_start: 0.7637 (mtm) cc_final: 0.7406 (mtp) REVERT: A 1102 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7515 (tmm) REVERT: A 1158 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7991 (tm) REVERT: A 1191 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6484 (pm20) REVERT: A 1460 LEU cc_start: 0.8459 (mm) cc_final: 0.8145 (mp) REVERT: B 416 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7762 (tpp80) REVERT: B 928 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8962 (pt) REVERT: B 1041 ILE cc_start: 0.9213 (mm) cc_final: 0.9009 (mm) REVERT: B 1172 MET cc_start: 0.8177 (mpp) cc_final: 0.7726 (mpp) REVERT: F 75 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7045 (mtm) REVERT: F 102 ILE cc_start: 0.8891 (mt) cc_final: 0.8476 (tt) REVERT: G 164 MET cc_start: 0.6961 (mmt) cc_final: 0.6667 (mmt) REVERT: H 123 MET cc_start: 0.9124 (tmm) cc_final: 0.8870 (tmm) REVERT: J 48 MET cc_start: 0.8992 (mmm) cc_final: 0.8360 (mmm) REVERT: K 85 GLU cc_start: 0.6855 (tp30) cc_final: 0.6518 (tp30) REVERT: L 56 ASP cc_start: 0.8113 (t0) cc_final: 0.7827 (t0) REVERT: U 31 SER cc_start: 0.5200 (OUTLIER) cc_final: 0.4225 (p) REVERT: V 365 MET cc_start: 0.7197 (pmm) cc_final: 0.6950 (pmm) REVERT: V 376 MET cc_start: 0.7272 (ptm) cc_final: 0.6763 (ptm) REVERT: V 420 MET cc_start: 0.7205 (mmm) cc_final: 0.6404 (mmt) REVERT: W 245 MET cc_start: 0.0558 (tmm) cc_final: -0.0213 (mtm) REVERT: W 439 ARG cc_start: 0.1789 (mmm160) cc_final: 0.1499 (mmm160) REVERT: a 61 MET cc_start: -0.2215 (ttt) cc_final: -0.3168 (tpt) REVERT: a 396 MET cc_start: -0.1853 (mtp) cc_final: -0.2480 (mtt) outliers start: 183 outliers final: 118 residues processed: 604 average time/residue: 0.5209 time to fit residues: 538.7305 Evaluate side-chains 534 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 408 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 367 VAL Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 233 HIS Chi-restraints excluded: chain W residue 285 THR Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 375 ARG Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 414 LEU Chi-restraints excluded: chain W residue 422 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 TRP Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 351 VAL Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 514 ILE Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 200 optimal weight: 5.9990 chunk 537 optimal weight: 20.0000 chunk 117 optimal weight: 0.4980 chunk 350 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 596 optimal weight: 40.0000 chunk 495 optimal weight: 0.6980 chunk 276 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 313 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN B 525 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS G 14 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN ** a 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 52083 Z= 0.220 Angle : 0.646 10.834 70834 Z= 0.327 Chirality : 0.044 0.344 7980 Planarity : 0.004 0.057 8828 Dihedral : 14.438 179.677 7811 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 2.96 % Allowed : 15.64 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 6120 helix: 1.27 (0.11), residues: 2454 sheet: -1.23 (0.17), residues: 779 loop : -0.95 (0.12), residues: 2887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1192 HIS 0.015 0.001 HIS A 313 PHE 0.038 0.001 PHE V 411 TYR 0.028 0.001 TYR a 539 ARG 0.010 0.000 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 444 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LEU cc_start: 0.8567 (mt) cc_final: 0.8281 (mt) REVERT: A 431 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.5485 (m-10) REVERT: A 499 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7667 (t0) REVERT: A 868 MET cc_start: 0.7602 (mtm) cc_final: 0.7355 (mtp) REVERT: A 1102 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7377 (ppp) REVERT: A 1158 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7965 (tm) REVERT: A 1191 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: A 1460 LEU cc_start: 0.8336 (mm) cc_final: 0.8063 (mp) REVERT: B 206 TYR cc_start: 0.7873 (m-80) cc_final: 0.7447 (m-10) REVERT: B 416 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7459 (tpp80) REVERT: B 928 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8963 (pt) REVERT: B 1041 ILE cc_start: 0.9188 (mm) cc_final: 0.8971 (mm) REVERT: F 102 ILE cc_start: 0.8769 (mt) cc_final: 0.8426 (tt) REVERT: G 164 MET cc_start: 0.6913 (mmt) cc_final: 0.6620 (mmt) REVERT: H 123 MET cc_start: 0.9089 (tmm) cc_final: 0.8750 (tmm) REVERT: I 118 HIS cc_start: 0.5702 (p-80) cc_final: 0.5465 (p-80) REVERT: J 48 MET cc_start: 0.8971 (mmm) cc_final: 0.8278 (mmm) REVERT: K 85 GLU cc_start: 0.6819 (tp30) cc_final: 0.6584 (tp30) REVERT: L 56 ASP cc_start: 0.8257 (t0) cc_final: 0.7863 (t0) REVERT: U 31 SER cc_start: 0.5117 (OUTLIER) cc_final: 0.4095 (p) REVERT: V 365 MET cc_start: 0.7258 (pmm) cc_final: 0.6939 (pmm) REVERT: V 420 MET cc_start: 0.6619 (mmm) cc_final: 0.6386 (mmt) REVERT: W 245 MET cc_start: 0.0425 (tmm) cc_final: -0.0117 (mtm) REVERT: Z 474 MET cc_start: 0.3298 (mmm) cc_final: 0.2517 (mmm) REVERT: a 61 MET cc_start: -0.2137 (ttt) cc_final: -0.3126 (tpt) REVERT: a 301 MET cc_start: -0.0659 (tpp) cc_final: -0.1111 (tpp) REVERT: a 396 MET cc_start: -0.1983 (mtp) cc_final: -0.2621 (mtt) REVERT: a 527 MET cc_start: 0.6606 (mmm) cc_final: 0.6242 (mpp) outliers start: 156 outliers final: 123 residues processed: 572 average time/residue: 0.4915 time to fit residues: 476.5405 Evaluate side-chains 539 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 408 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 367 VAL Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 233 HIS Chi-restraints excluded: chain W residue 285 THR Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 375 ARG Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 414 LEU Chi-restraints excluded: chain W residue 422 VAL Chi-restraints excluded: chain W residue 455 LEU Chi-restraints excluded: chain W residue 508 TYR Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 TRP Chi-restraints excluded: chain Z residue 264 LEU Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 351 VAL Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 514 ILE Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 575 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 340 optimal weight: 0.9980 chunk 435 optimal weight: 20.0000 chunk 337 optimal weight: 0.8980 chunk 502 optimal weight: 20.0000 chunk 333 optimal weight: 0.8980 chunk 594 optimal weight: 7.9990 chunk 372 optimal weight: 0.8980 chunk 362 optimal weight: 0.3980 chunk 274 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN ** a 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 52083 Z= 0.187 Angle : 0.633 11.638 70834 Z= 0.319 Chirality : 0.043 0.273 7980 Planarity : 0.004 0.057 8828 Dihedral : 14.318 178.836 7811 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 2.75 % Allowed : 16.27 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 6120 helix: 1.36 (0.11), residues: 2457 sheet: -1.15 (0.18), residues: 775 loop : -0.91 (0.12), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1192 HIS 0.034 0.001 HIS A 313 PHE 0.032 0.001 PHE V 411 TYR 0.019 0.001 TYR a 539 ARG 0.010 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 440 time to evaluate : 4.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LEU cc_start: 0.8564 (mt) cc_final: 0.8230 (mt) REVERT: A 431 PHE cc_start: 0.5831 (OUTLIER) cc_final: 0.5545 (m-10) REVERT: A 469 MET cc_start: 0.7571 (ttm) cc_final: 0.7275 (ttm) REVERT: A 499 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7448 (t0) REVERT: A 868 MET cc_start: 0.7557 (mtm) cc_final: 0.7322 (mtp) REVERT: A 1102 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7338 (ppp) REVERT: A 1158 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7932 (tm) REVERT: A 1191 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6775 (pm20) REVERT: A 1460 LEU cc_start: 0.8226 (mm) cc_final: 0.8000 (mp) REVERT: B 206 TYR cc_start: 0.7861 (m-80) cc_final: 0.7488 (m-10) REVERT: B 416 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7507 (tpp80) REVERT: B 908 MET cc_start: 0.8001 (tmm) cc_final: 0.7760 (tmm) REVERT: B 981 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8816 (mt) REVERT: B 1041 ILE cc_start: 0.9186 (mm) cc_final: 0.8978 (mm) REVERT: B 1054 MET cc_start: 0.8326 (mmt) cc_final: 0.8097 (mmt) REVERT: B 1172 MET cc_start: 0.8391 (mmm) cc_final: 0.7820 (mpp) REVERT: C 263 LEU cc_start: 0.8539 (tp) cc_final: 0.8179 (tt) REVERT: E 120 ASP cc_start: 0.6807 (m-30) cc_final: 0.6456 (m-30) REVERT: F 102 ILE cc_start: 0.8662 (mt) cc_final: 0.8339 (tt) REVERT: G 164 MET cc_start: 0.6913 (mmt) cc_final: 0.6630 (mmt) REVERT: H 123 MET cc_start: 0.8993 (tmm) cc_final: 0.8643 (tmm) REVERT: J 48 MET cc_start: 0.8935 (mmm) cc_final: 0.8236 (mmm) REVERT: K 85 GLU cc_start: 0.6780 (tp30) cc_final: 0.6513 (tp30) REVERT: L 41 TYR cc_start: 0.5906 (t80) cc_final: 0.5689 (t80) REVERT: U 31 SER cc_start: 0.5165 (OUTLIER) cc_final: 0.4121 (p) REVERT: V 365 MET cc_start: 0.7274 (pmm) cc_final: 0.7026 (pmm) REVERT: W 245 MET cc_start: 0.0345 (tmm) cc_final: -0.0118 (mtm) REVERT: Y 42 MET cc_start: 0.4629 (mmt) cc_final: 0.4403 (mmp) REVERT: Z 474 MET cc_start: 0.2631 (mmm) cc_final: 0.2259 (mmm) REVERT: a 61 MET cc_start: -0.1928 (ttt) cc_final: -0.3014 (tpt) REVERT: a 301 MET cc_start: 0.0088 (tpp) cc_final: -0.0482 (tpp) REVERT: a 396 MET cc_start: -0.1989 (mtp) cc_final: -0.2623 (mtt) outliers start: 145 outliers final: 108 residues processed: 555 average time/residue: 0.4917 time to fit residues: 463.0442 Evaluate side-chains 523 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 407 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1111 SER Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 367 VAL Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 233 HIS Chi-restraints excluded: chain W residue 237 THR Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 414 LEU Chi-restraints excluded: chain W residue 422 VAL Chi-restraints excluded: chain W residue 455 LEU Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 TRP Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 351 VAL Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 514 ILE Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 367 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 378 optimal weight: 0.8980 chunk 405 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 467 optimal weight: 50.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 52083 Z= 0.294 Angle : 0.675 12.364 70834 Z= 0.341 Chirality : 0.044 0.245 7980 Planarity : 0.004 0.062 8828 Dihedral : 14.243 179.905 7810 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 2.79 % Allowed : 16.65 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 6120 helix: 1.38 (0.11), residues: 2454 sheet: -1.13 (0.18), residues: 771 loop : -0.89 (0.12), residues: 2895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 293 HIS 0.022 0.001 HIS G 14 PHE 0.034 0.002 PHE B 356 TYR 0.021 0.001 TYR a 539 ARG 0.008 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 412 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LEU cc_start: 0.8551 (mt) cc_final: 0.8310 (mt) REVERT: A 469 MET cc_start: 0.7804 (ttm) cc_final: 0.7559 (ttm) REVERT: A 499 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7590 (t0) REVERT: A 520 MET cc_start: 0.8021 (mmp) cc_final: 0.7779 (mmp) REVERT: A 538 VAL cc_start: 0.8068 (t) cc_final: 0.7765 (m) REVERT: A 868 MET cc_start: 0.7503 (mtm) cc_final: 0.7292 (mtp) REVERT: A 1102 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7415 (ppp) REVERT: A 1158 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8259 (tm) REVERT: A 1191 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: A 1463 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8786 (tt) REVERT: B 206 TYR cc_start: 0.7952 (m-80) cc_final: 0.7570 (m-10) REVERT: B 416 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7568 (tpp80) REVERT: B 1041 ILE cc_start: 0.9240 (mm) cc_final: 0.9029 (mm) REVERT: B 1172 MET cc_start: 0.8404 (mmm) cc_final: 0.7917 (mpp) REVERT: F 102 ILE cc_start: 0.8761 (mt) cc_final: 0.8434 (tt) REVERT: J 48 MET cc_start: 0.9023 (mmm) cc_final: 0.8396 (mmm) REVERT: K 85 GLU cc_start: 0.6908 (tp30) cc_final: 0.6583 (tp30) REVERT: U 31 SER cc_start: 0.5382 (OUTLIER) cc_final: 0.4346 (p) REVERT: V 345 LEU cc_start: 0.8053 (mt) cc_final: 0.7774 (mt) REVERT: V 420 MET cc_start: 0.6735 (mmm) cc_final: 0.6258 (mmp) REVERT: W 245 MET cc_start: 0.0607 (tmm) cc_final: 0.0174 (mtm) REVERT: Z 474 MET cc_start: 0.3122 (mmm) cc_final: 0.2682 (mmm) REVERT: a 30 MET cc_start: -0.2876 (OUTLIER) cc_final: -0.3211 (mtt) REVERT: a 61 MET cc_start: -0.1769 (ttt) cc_final: -0.2937 (tpt) REVERT: a 301 MET cc_start: 0.0765 (tpp) cc_final: 0.0139 (tpp) REVERT: a 396 MET cc_start: -0.1985 (mtp) cc_final: -0.2626 (mtt) outliers start: 147 outliers final: 116 residues processed: 530 average time/residue: 0.4800 time to fit residues: 431.4710 Evaluate side-chains 521 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 397 time to evaluate : 4.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 233 HIS Chi-restraints excluded: chain W residue 237 THR Chi-restraints excluded: chain W residue 285 THR Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 375 ARG Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 414 LEU Chi-restraints excluded: chain W residue 422 VAL Chi-restraints excluded: chain W residue 455 LEU Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 TRP Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain a residue 30 MET Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 351 VAL Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 514 ILE Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 540 optimal weight: 40.0000 chunk 569 optimal weight: 50.0000 chunk 519 optimal weight: 7.9990 chunk 554 optimal weight: 30.0000 chunk 333 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 chunk 435 optimal weight: 20.0000 chunk 170 optimal weight: 4.9990 chunk 500 optimal weight: 4.9990 chunk 524 optimal weight: 5.9990 chunk 552 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 416 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 447 HIS ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.177 52083 Z= 0.426 Angle : 0.762 13.255 70834 Z= 0.386 Chirality : 0.046 0.279 7980 Planarity : 0.005 0.064 8828 Dihedral : 14.259 178.938 7810 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.88 % Rotamer: Outliers : 3.26 % Allowed : 16.70 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 6120 helix: 1.21 (0.11), residues: 2460 sheet: -1.26 (0.18), residues: 769 loop : -0.95 (0.12), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 293 HIS 0.025 0.002 HIS G 14 PHE 0.030 0.002 PHE a 535 TYR 0.040 0.002 TYR L 41 ARG 0.008 0.001 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 403 time to evaluate : 4.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LEU cc_start: 0.8632 (mt) cc_final: 0.8424 (mt) REVERT: A 469 MET cc_start: 0.7830 (ttm) cc_final: 0.7472 (ttm) REVERT: A 538 VAL cc_start: 0.8007 (t) cc_final: 0.7727 (m) REVERT: A 868 MET cc_start: 0.7637 (mtm) cc_final: 0.7436 (mtp) REVERT: A 1102 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7814 (tmm) REVERT: B 206 TYR cc_start: 0.8207 (m-80) cc_final: 0.7758 (m-10) REVERT: B 416 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7612 (tpp80) REVERT: B 447 SER cc_start: 0.8487 (m) cc_final: 0.8090 (t) REVERT: B 928 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9080 (pt) REVERT: B 1041 ILE cc_start: 0.9366 (mm) cc_final: 0.9153 (mm) REVERT: B 1172 MET cc_start: 0.8273 (mmm) cc_final: 0.7955 (mpp) REVERT: G 14 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7776 (t70) REVERT: H 123 MET cc_start: 0.9174 (tmm) cc_final: 0.8937 (tmm) REVERT: J 48 MET cc_start: 0.9026 (mmm) cc_final: 0.8569 (mmm) REVERT: U 31 SER cc_start: 0.5788 (OUTLIER) cc_final: 0.4814 (p) REVERT: V 243 MET cc_start: 0.7398 (mmm) cc_final: 0.6978 (mmp) REVERT: V 420 MET cc_start: 0.6911 (mmm) cc_final: 0.6444 (mmp) REVERT: W 245 MET cc_start: 0.1267 (tmm) cc_final: 0.0735 (mtm) REVERT: W 299 MET cc_start: 0.6550 (mmt) cc_final: 0.6136 (mmm) REVERT: Z 254 MET cc_start: 0.2446 (tmm) cc_final: 0.2179 (mmm) REVERT: Z 474 MET cc_start: 0.3321 (mmm) cc_final: 0.2885 (mmm) REVERT: a 30 MET cc_start: -0.2767 (OUTLIER) cc_final: -0.3174 (mtt) REVERT: a 61 MET cc_start: -0.1867 (ttt) cc_final: -0.3028 (tpt) REVERT: a 145 MET cc_start: -0.0567 (mpp) cc_final: -0.1316 (mtm) REVERT: a 301 MET cc_start: 0.0816 (tpp) cc_final: 0.0261 (tpp) REVERT: a 396 MET cc_start: -0.2005 (mtp) cc_final: -0.2650 (mtt) REVERT: a 437 MET cc_start: -0.1334 (mmt) cc_final: -0.3001 (mmt) outliers start: 172 outliers final: 130 residues processed: 539 average time/residue: 0.4998 time to fit residues: 459.3060 Evaluate side-chains 524 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 388 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1362 ILE Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 233 HIS Chi-restraints excluded: chain W residue 237 THR Chi-restraints excluded: chain W residue 285 THR Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 375 ARG Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 414 LEU Chi-restraints excluded: chain W residue 422 VAL Chi-restraints excluded: chain W residue 425 MET Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 TRP Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 451 MET Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain a residue 30 MET Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 351 VAL Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 514 ILE Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 363 optimal weight: 0.8980 chunk 586 optimal weight: 50.0000 chunk 357 optimal weight: 0.8980 chunk 277 optimal weight: 0.9990 chunk 407 optimal weight: 8.9990 chunk 614 optimal weight: 3.9990 chunk 565 optimal weight: 5.9990 chunk 489 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 378 optimal weight: 0.9990 chunk 300 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1313 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 461 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS G 14 HIS H 130 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 HIS ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 75 GLN ** a 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 52083 Z= 0.200 Angle : 0.697 17.600 70834 Z= 0.347 Chirality : 0.044 0.230 7980 Planarity : 0.004 0.057 8828 Dihedral : 14.144 177.261 7810 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 2.00 % Allowed : 18.20 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 6120 helix: 1.33 (0.11), residues: 2452 sheet: -1.14 (0.18), residues: 772 loop : -0.84 (0.12), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1192 HIS 0.019 0.001 HIS A 313 PHE 0.034 0.001 PHE E 73 TYR 0.040 0.001 TYR L 41 ARG 0.006 0.000 ARG A 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12240 Ramachandran restraints generated. 6120 Oldfield, 0 Emsley, 6120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 425 time to evaluate : 4.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LEU cc_start: 0.8599 (mt) cc_final: 0.8367 (mt) REVERT: A 469 MET cc_start: 0.7389 (ttm) cc_final: 0.7014 (ttm) REVERT: A 499 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7494 (t0) REVERT: A 538 VAL cc_start: 0.7814 (t) cc_final: 0.7501 (m) REVERT: A 868 MET cc_start: 0.7484 (mtm) cc_final: 0.7266 (mtp) REVERT: A 1102 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7869 (tmm) REVERT: A 1191 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6858 (pm20) REVERT: B 108 MET cc_start: 0.8052 (ttp) cc_final: 0.7757 (ptt) REVERT: B 206 TYR cc_start: 0.7981 (m-80) cc_final: 0.7643 (m-10) REVERT: B 416 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7621 (tpp80) REVERT: B 447 SER cc_start: 0.8465 (m) cc_final: 0.8225 (t) REVERT: B 1041 ILE cc_start: 0.9242 (mm) cc_final: 0.9033 (mm) REVERT: B 1151 MET cc_start: 0.8392 (tmm) cc_final: 0.7286 (ttp) REVERT: B 1161 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6899 (mt-10) REVERT: B 1172 MET cc_start: 0.8177 (mmm) cc_final: 0.7800 (mpp) REVERT: E 135 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7782 (mm) REVERT: H 123 MET cc_start: 0.8987 (tmm) cc_final: 0.8729 (tmm) REVERT: I 108 MET cc_start: 0.7250 (mmp) cc_final: 0.7046 (mmp) REVERT: J 48 MET cc_start: 0.8980 (mmm) cc_final: 0.8351 (mmm) REVERT: U 31 SER cc_start: 0.5626 (OUTLIER) cc_final: 0.4650 (p) REVERT: V 243 MET cc_start: 0.7340 (mmm) cc_final: 0.6925 (mmp) REVERT: W 245 MET cc_start: 0.1046 (tmm) cc_final: 0.0525 (mtm) REVERT: W 299 MET cc_start: 0.6620 (mmt) cc_final: 0.6229 (mmm) REVERT: a 30 MET cc_start: -0.2419 (OUTLIER) cc_final: -0.3122 (mtt) REVERT: a 61 MET cc_start: -0.1886 (ttt) cc_final: -0.2989 (tpt) REVERT: a 145 MET cc_start: -0.0658 (mpp) cc_final: -0.1321 (mtm) REVERT: a 301 MET cc_start: 0.1051 (tpp) cc_final: 0.0496 (tpp) REVERT: a 396 MET cc_start: -0.1891 (mtp) cc_final: -0.2496 (mtt) REVERT: a 437 MET cc_start: -0.1370 (mmt) cc_final: -0.3020 (mmt) outliers start: 105 outliers final: 84 residues processed: 514 average time/residue: 0.4856 time to fit residues: 424.3588 Evaluate side-chains 489 residues out of total 5477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 398 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 25 GLU Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain W residue 233 HIS Chi-restraints excluded: chain W residue 285 THR Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 375 ARG Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 414 LEU Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 70 TRP Chi-restraints excluded: chain Z residue 183 LYS Chi-restraints excluded: chain Z residue 451 MET Chi-restraints excluded: chain a residue 30 MET Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 351 VAL Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 481 LEU Chi-restraints excluded: chain a residue 535 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 617 random chunks: chunk 388 optimal weight: 8.9990 chunk 521 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 451 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 490 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 503 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS H 87 GLN H 130 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 447 HIS W 502 HIS ** a 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.113003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.069264 restraints weight = 229654.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.072113 restraints weight = 106196.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071797 restraints weight = 54667.507| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 52083 Z= 0.361 Angle : 0.735 12.093 70834 Z= 0.370 Chirality : 0.045 0.304 7980 Planarity : 0.005 0.065 8828 Dihedral : 14.132 178.808 7806 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 2.06 % Allowed : 18.18 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 6120 helix: 1.32 (0.11), residues: 2448 sheet: -1.13 (0.18), residues: 765 loop : -0.91 (0.12), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP a 293 HIS 0.008 0.001 HIS B 577 PHE 0.030 0.002 PHE a 535 TYR 0.033 0.002 TYR L 41 ARG 0.005 0.001 ARG a 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10182.41 seconds wall clock time: 180 minutes 7.04 seconds (10807.04 seconds total)