Starting phenix.real_space_refine on Tue Jul 7 03:57:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9can_45397/07_2026/9can_45397_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9can_45397/07_2026/9can_45397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9can_45397/07_2026/9can_45397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9can_45397/07_2026/9can_45397.map" model { file = "/net/cci-nas-00/data/ceres_data/9can_45397/07_2026/9can_45397_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9can_45397/07_2026/9can_45397_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 114 5.16 5 C 25693 2.51 5 N 7451 2.21 5 O 8639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42187 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 759 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 781 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2864 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "J" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2835 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "Q" Number of atoms: 5289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5289 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 30, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3548 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Chain: "T" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3336 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} 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 Chain: "V" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} 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 Chain: "X" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "Y" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 367 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.35, per 1000 atoms: 0.22 Number of scatterers: 42187 At special positions: 0 Unit cell: (127.143, 177.834, 219.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 290 15.00 O 8639 8.00 N 7451 7.00 C 25693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8706 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 36 sheets defined 48.8% alpha, 10.0% beta 131 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.893A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.598A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.294A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 4.349A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.759A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.160A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 4.568A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.850A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 80 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.854A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.535A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.893A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.976A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.855A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.591A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.255A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.633A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 98 removed outlier: 3.939A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 121 removed outlier: 4.106A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 709 through 724 Processing helix chain 'Q' and resid 736 through 753 removed outlier: 3.698A pdb=" N GLN Q 740 " --> pdb=" O GLY Q 736 " (cutoff:3.500A) Processing helix chain 'Q' and resid 763 through 777 removed outlier: 4.711A pdb=" N HIS Q 768 " --> pdb=" O ALA Q 764 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN Q 769 " --> pdb=" O SER Q 765 " (cutoff:3.500A) Processing helix chain 'Q' and resid 789 through 800 Processing helix chain 'Q' and resid 819 through 825 Processing helix chain 'Q' and resid 826 through 831 removed outlier: 3.560A pdb=" N GLN Q 831 " --> pdb=" O ALA Q 827 " (cutoff:3.500A) Processing helix chain 'Q' and resid 842 through 847 removed outlier: 4.197A pdb=" N ALA Q 845 " --> pdb=" O GLU Q 842 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE Q 846 " --> pdb=" O ALA Q 843 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS Q 847 " --> pdb=" O GLN Q 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 842 through 847' Processing helix chain 'Q' and resid 851 through 859 Processing helix chain 'Q' and resid 878 through 888 Processing helix chain 'Q' and resid 894 through 901 removed outlier: 3.880A pdb=" N PHE Q 898 " --> pdb=" O SER Q 894 " (cutoff:3.500A) Processing helix chain 'Q' and resid 920 through 926 removed outlier: 4.228A pdb=" N HIS Q 925 " --> pdb=" O LEU Q 921 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET Q 926 " --> pdb=" O ARG Q 922 " (cutoff:3.500A) Processing helix chain 'Q' and resid 957 through 970 removed outlier: 3.619A pdb=" N LYS Q 962 " --> pdb=" O GLN Q 958 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU Q 963 " --> pdb=" O ARG Q 959 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR Q 964 " --> pdb=" O GLN Q 960 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN Q 965 " --> pdb=" O ALA Q 961 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN Q 970 " --> pdb=" O VAL Q 966 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1003 through 1007 removed outlier: 3.558A pdb=" N GLN Q1006 " --> pdb=" O ALA Q1003 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE Q1007 " --> pdb=" O VAL Q1004 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1003 through 1007' Processing helix chain 'Q' and resid 1008 through 1013 removed outlier: 3.825A pdb=" N ASN Q1012 " --> pdb=" O ARG Q1008 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1014 through 1017 Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 4.009A pdb=" N TYR Q1090 " --> pdb=" O PRO Q1086 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1101 through 1111 Processing helix chain 'Q' and resid 1121 through 1133 Processing helix chain 'Q' and resid 1138 through 1145 Processing helix chain 'Q' and resid 1147 through 1154 removed outlier: 3.508A pdb=" N GLU Q1154 " --> pdb=" O LYS Q1150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1169 through 1178 removed outlier: 3.694A pdb=" N VAL Q1177 " --> pdb=" O GLU Q1173 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1185 through 1191 Processing helix chain 'Q' and resid 1192 through 1201 Processing helix chain 'Q' and resid 1226 through 1238 removed outlier: 3.674A pdb=" N THR Q1230 " --> pdb=" O SER Q1226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1290 through 1297 removed outlier: 3.564A pdb=" N GLU Q1297 " --> pdb=" O ARG Q1293 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1298 through 1315 removed outlier: 3.677A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY Q1315 " --> pdb=" O LEU Q1311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1326 through 1338 removed outlier: 5.197A pdb=" N GLU Q1332 " --> pdb=" O MET Q1328 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU Q1333 " --> pdb=" O ASP Q1329 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR Q1337 " --> pdb=" O GLU Q1333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1351 through 1364 removed outlier: 4.065A pdb=" N ARG Q1355 " --> pdb=" O LEU Q1351 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP Q1356 " --> pdb=" O GLU Q1352 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1397 through 1409 removed outlier: 3.688A pdb=" N ALA Q1408 " --> pdb=" O ALA Q1404 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1446 removed outlier: 4.172A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 34 removed outlier: 3.551A pdb=" N ALA R 33 " --> pdb=" O GLU R 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR R 34 " --> pdb=" O GLN R 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 30 through 34' Processing helix chain 'R' and resid 84 through 87 Processing helix chain 'R' and resid 89 through 95 Processing helix chain 'R' and resid 108 through 121 Processing helix chain 'R' and resid 143 through 157 removed outlier: 3.596A pdb=" N ARG R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 206 through 209 removed outlier: 3.501A pdb=" N ALA R 209 " --> pdb=" O LEU R 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 206 through 209' Processing helix chain 'R' and resid 215 through 231 Processing helix chain 'R' and resid 239 through 250 Processing helix chain 'R' and resid 256 through 261 Processing helix chain 'R' and resid 266 through 271 removed outlier: 3.719A pdb=" N ASP R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 589 through 597 removed outlier: 3.567A pdb=" N LEU R 593 " --> pdb=" O SER R 589 " (cutoff:3.500A) Processing helix chain 'R' and resid 607 through 609 No H-bonds generated for 'chain 'R' and resid 607 through 609' Processing helix chain 'R' and resid 616 through 621 Processing helix chain 'R' and resid 622 through 627 removed outlier: 4.298A pdb=" N PHE R 626 " --> pdb=" O PRO R 622 " (cutoff:3.500A) Processing helix chain 'R' and resid 637 through 649 removed outlier: 3.570A pdb=" N LYS R 648 " --> pdb=" O THR R 644 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS R 649 " --> pdb=" O ILE R 645 " (cutoff:3.500A) Processing helix chain 'R' and resid 658 through 666 Processing helix chain 'R' and resid 672 through 676 removed outlier: 3.798A pdb=" N ALA R 675 " --> pdb=" O GLY R 672 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 672 through 676' Processing helix chain 'R' and resid 679 through 692 Processing helix chain 'R' and resid 708 through 720 Processing helix chain 'R' and resid 720 through 725 removed outlier: 3.773A pdb=" N ARG R 725 " --> pdb=" O GLU R 721 " (cutoff:3.500A) Processing helix chain 'R' and resid 731 through 738 Processing helix chain 'S' and resid 29 through 40 removed outlier: 4.379A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 83 removed outlier: 4.105A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 104 removed outlier: 3.774A pdb=" N GLU S 104 " --> pdb=" O TYR S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 removed outlier: 3.818A pdb=" N TYR S 140 " --> pdb=" O ASN S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 156 removed outlier: 4.355A pdb=" N GLU S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.677A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 116 through 126 Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 217 through 219 No H-bonds generated for 'chain 'T' and resid 217 through 219' Processing helix chain 'T' and resid 249 through 256 removed outlier: 3.536A pdb=" N ASN T 256 " --> pdb=" O LEU T 252 " (cutoff:3.500A) Processing helix chain 'T' and resid 282 through 298 removed outlier: 3.866A pdb=" N GLN T 286 " --> pdb=" O GLU T 282 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU T 287 " --> pdb=" O LYS T 283 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 Processing helix chain 'T' and resid 317 through 328 Processing helix chain 'T' and resid 360 through 365 removed outlier: 3.585A pdb=" N ASP T 365 " --> pdb=" O PRO T 361 " (cutoff:3.500A) Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 418 Processing helix chain 'T' and resid 418 through 429 removed outlier: 3.698A pdb=" N SER T 429 " --> pdb=" O LEU T 425 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 458 removed outlier: 3.533A pdb=" N THR T 458 " --> pdb=" O LYS T 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 93 removed outlier: 3.779A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.739A pdb=" N LYS U 181 " --> pdb=" O ASP U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 209 No H-bonds generated for 'chain 'U' and resid 207 through 209' Processing helix chain 'U' and resid 241 through 250 removed outlier: 3.763A pdb=" N ARG U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 260 Processing helix chain 'U' and resid 266 through 284 removed outlier: 3.748A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 301 removed outlier: 3.650A pdb=" N MET U 300 " --> pdb=" O GLU U 297 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 313 Processing helix chain 'U' and resid 344 through 349 Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 4.256A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 432 through 443 Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.556A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.504A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 127 Processing helix chain 'V' and resid 184 through 193 removed outlier: 3.835A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 216 through 219 Processing helix chain 'V' and resid 249 through 258 removed outlier: 3.505A pdb=" N ARG V 258 " --> pdb=" O VAL V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 273 removed outlier: 3.872A pdb=" N MET V 268 " --> pdb=" O ASP V 264 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.718A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 313 through 316 Processing helix chain 'V' and resid 317 through 328 Processing helix chain 'V' and resid 360 through 365 Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 418 Processing helix chain 'V' and resid 419 through 429 Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.646A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 93 removed outlier: 3.694A pdb=" N GLY W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 123 Processing helix chain 'W' and resid 172 through 181 Processing helix chain 'W' and resid 241 through 250 removed outlier: 4.018A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.524A pdb=" N ALA W 256 " --> pdb=" O GLN W 252 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.513A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.848A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 343 Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.684A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 removed outlier: 3.502A pdb=" N ILE W 364 " --> pdb=" O ASN W 360 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.834A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 Processing helix chain 'W' and resid 432 through 442 removed outlier: 3.717A pdb=" N GLU W 442 " --> pdb=" O LYS W 438 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.665A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 116 through 127 Processing helix chain 'X' and resid 182 through 192 removed outlier: 3.780A pdb=" N TYR X 186 " --> pdb=" O ASP X 182 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 271 removed outlier: 4.061A pdb=" N GLN X 271 " --> pdb=" O SER X 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 Processing helix chain 'X' and resid 313 through 316 Processing helix chain 'X' and resid 317 through 328 removed outlier: 3.510A pdb=" N PHE X 321 " --> pdb=" O ASP X 317 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 417 removed outlier: 3.541A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 428 removed outlier: 3.538A pdb=" N CYS X 422 " --> pdb=" O LEU X 418 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 removed outlier: 3.634A pdb=" N THR X 458 " --> pdb=" O LYS X 454 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 removed outlier: 3.598A pdb=" N ALA Y 85 " --> pdb=" O LYS Y 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 107 removed outlier: 3.828A pdb=" N PHE Y 107 " --> pdb=" O SER Y 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 104 through 107' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 255 through 260 Processing helix chain 'Y' and resid 267 through 283 removed outlier: 3.547A pdb=" N GLN Y 272 " --> pdb=" O GLU Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 Processing helix chain 'Y' and resid 302 through 313 removed outlier: 4.118A pdb=" N ARG Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.687A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN Y 407 " --> pdb=" O ILE Y 403 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE Y 409 " --> pdb=" O VAL Y 405 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.585A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 443 Processing helix chain 'Y' and resid 444 through 447 Processing helix chain 'Z' and resid 255 through 277 Processing sheet with id=AA1, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA2, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.585A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.375A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Q' and resid 728 through 729 removed outlier: 3.585A pdb=" N LEU Q 729 " --> pdb=" O LEU Q 867 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET Q 838 " --> pdb=" O LEU Q 866 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU Q 868 " --> pdb=" O MET Q 838 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU Q 840 " --> pdb=" O LEU Q 868 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 948 through 954 removed outlier: 3.769A pdb=" N VAL Q1389 " --> pdb=" O THR Q1418 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU Q1422 " --> pdb=" O PHE Q1391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 5.991A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Q' and resid 1071 through 1073 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1073 current: chain 'X' and resid 163 through 172 removed outlier: 3.726A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 209 through 215 removed outlier: 6.022A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 3.738A pdb=" N GLU Q1222 " --> pdb=" O TYR Q1083 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 14 through 15 removed outlier: 6.818A pdb=" N VAL R 14 " --> pdb=" O GLU R 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 62 through 64 removed outlier: 3.705A pdb=" N ARG R 50 " --> pdb=" O ASP R 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE R 40 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N THR R 137 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ILE R 42 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR R 164 " --> pdb=" O ILE R 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 67 through 71 Processing sheet with id=AB3, first strand: chain 'R' and resid 100 through 101 removed outlier: 3.597A pdb=" N PHE R 104 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 184 through 189 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 203 through 204 current: chain 'R' and resid 700 through 702 Processing sheet with id=AB5, first strand: chain 'S' and resid 125 through 126 Processing sheet with id=AB6, first strand: chain 'T' and resid 44 through 45 removed outlier: 3.517A pdb=" N GLU T 45 " --> pdb=" O PHE T 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.226A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER T 340 " --> pdb=" O LEU T 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 129 through 151 removed outlier: 6.567A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP T 151 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE T 163 " --> pdb=" O ASP T 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 175 through 181 current: chain 'T' and resid 209 through 215 removed outlier: 5.944A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AC1, first strand: chain 'T' and resid 394 through 395 removed outlier: 7.316A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.643A pdb=" N SER U 41 " --> pdb=" O MET U 44 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET U 44 " --> pdb=" O SER U 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.330A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU U 293 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA U 324 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE U 295 " --> pdb=" O ALA U 324 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 125 through 147 removed outlier: 5.037A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU U 142 " --> pdb=" O THR U 159 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 199 through 205 removed outlier: 5.346A pdb=" N VAL U 222 " --> pdb=" O LEU U 202 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ARG U 204 " --> pdb=" O VAL U 222 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 329 through 331 Processing sheet with id=AC6, first strand: chain 'V' and resid 102 through 106 removed outlier: 3.702A pdb=" N SER V 340 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY V 79 " --> pdb=" O SER V 340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 129 through 151 removed outlier: 6.609A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N HIS V 165 " --> pdb=" O PRO V 149 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP V 151 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE V 163 " --> pdb=" O ASP V 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 175 through 181 current: chain 'V' and resid 207 through 214 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 207 through 214 current: chain 'W' and resid 154 through 161 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 168 current: chain 'W' and resid 199 through 204 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 199 through 204 current: chain 'Z' and resid 315 through 319 Processing sheet with id=AC8, first strand: chain 'V' and resid 344 through 345 removed outlier: 3.597A pdb=" N SER V 355 " --> pdb=" O THR V 345 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AD1, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.315A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL W 71 " --> pdb=" O MET W 323 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR W 325 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL W 73 " --> pdb=" O THR W 325 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AD3, first strand: chain 'X' and resid 44 through 45 removed outlier: 3.664A pdb=" N GLU X 45 " --> pdb=" O PHE X 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.330A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY X 79 " --> pdb=" O SER X 340 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR X 372 " --> pdb=" O LEU X 76 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA X 78 " --> pdb=" O THR X 372 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 344 through 346 removed outlier: 3.552A pdb=" N SER X 355 " --> pdb=" O THR X 345 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 40 through 41 removed outlier: 3.540A pdb=" N SER Y 41 " --> pdb=" O MET Y 44 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.281A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 125 through 147 removed outlier: 6.998A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 171 current: chain 'Y' and resid 199 through 204 Processing sheet with id=AD9, first strand: chain 'Y' and resid 330 through 331 1566 hydrogen bonds defined for protein. 4617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 334 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 12.66 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11081 1.33 - 1.46: 11058 1.46 - 1.58: 20523 1.58 - 1.71: 573 1.71 - 1.83: 203 Bond restraints: 43438 Sorted by residual: bond pdb=" C1' DT I -61 " pdb=" N1 DT I -61 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" C1' DC I 37 " pdb=" N1 DC I 37 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.69e+01 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.53e+01 bond pdb=" CB PRO R 59 " pdb=" CG PRO R 59 " ideal model delta sigma weight residual 1.492 1.659 -0.167 5.00e-02 4.00e+02 1.12e+01 ... (remaining 43433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 59484 3.88 - 7.77: 379 7.77 - 11.65: 66 11.65 - 15.53: 23 15.53 - 19.41: 7 Bond angle restraints: 59959 Sorted by residual: angle pdb=" CA PRO R 59 " pdb=" N PRO R 59 " pdb=" CD PRO R 59 " ideal model delta sigma weight residual 112.00 95.18 16.82 1.40e+00 5.10e-01 1.44e+02 angle pdb=" CA MET Q 833 " pdb=" CB MET Q 833 " pdb=" CG MET Q 833 " ideal model delta sigma weight residual 114.10 126.90 -12.80 2.00e+00 2.50e-01 4.10e+01 angle pdb=" O4' DC I -58 " pdb=" C1' DC I -58 " pdb=" N1 DC I -58 " ideal model delta sigma weight residual 108.00 112.45 -4.45 7.00e-01 2.04e+00 4.04e+01 angle pdb=" CA MET H 59 " pdb=" CB MET H 59 " pdb=" CG MET H 59 " ideal model delta sigma weight residual 114.10 126.51 -12.41 2.00e+00 2.50e-01 3.85e+01 angle pdb=" CB MET Q 816 " pdb=" CG MET Q 816 " pdb=" SD MET Q 816 " ideal model delta sigma weight residual 112.70 131.29 -18.59 3.00e+00 1.11e-01 3.84e+01 ... (remaining 59954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 23602 35.99 - 71.98: 2065 71.98 - 107.97: 80 107.97 - 143.96: 5 143.96 - 179.95: 4 Dihedral angle restraints: 25756 sinusoidal: 12277 harmonic: 13479 Sorted by residual: dihedral pdb=" O1B ADP W1001 " pdb=" O3A ADP W1001 " pdb=" PB ADP W1001 " pdb=" PA ADP W1001 " ideal model delta sinusoidal sigma weight residual 300.00 133.28 166.72 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' ADP W1001 " pdb=" O5' ADP W1001 " pdb=" PA ADP W1001 " pdb=" O2A ADP W1001 " ideal model delta sinusoidal sigma weight residual 300.00 163.42 136.58 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" C5' ADP T1001 " pdb=" O5' ADP T1001 " pdb=" PA ADP T1001 " pdb=" O2A ADP T1001 " ideal model delta sinusoidal sigma weight residual -60.00 -178.73 118.73 1 2.00e+01 2.50e-03 3.55e+01 ... (remaining 25753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 6542 0.105 - 0.210: 387 0.210 - 0.316: 28 0.316 - 0.421: 3 0.421 - 0.526: 2 Chirality restraints: 6962 Sorted by residual: chirality pdb=" CG LEU U 111 " pdb=" CB LEU U 111 " pdb=" CD1 LEU U 111 " pdb=" CD2 LEU U 111 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CB VAL D 38 " pdb=" CA VAL D 38 " pdb=" CG1 VAL D 38 " pdb=" CG2 VAL D 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CB ILE H 86 " pdb=" CA ILE H 86 " pdb=" CG1 ILE H 86 " pdb=" CG2 ILE H 86 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 6959 not shown) Planarity restraints: 6690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 58 " -0.125 5.00e-02 4.00e+02 1.73e-01 4.81e+01 pdb=" N PRO R 59 " 0.299 5.00e-02 4.00e+02 pdb=" CA PRO R 59 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO R 59 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 72 " -0.426 9.50e-02 1.11e+02 1.91e-01 2.23e+01 pdb=" NE ARG A 72 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 72 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 72 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 72 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO G 80 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.050 5.00e-02 4.00e+02 ... (remaining 6687 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 7 2.29 - 2.94: 17418 2.94 - 3.60: 63374 3.60 - 4.25: 101971 4.25 - 4.90: 162536 Nonbonded interactions: 345306 Sorted by model distance: nonbonded pdb=" NE2 GLN E 68 " pdb=" NH2 ARG E 72 " model vdw 1.638 3.200 nonbonded pdb=" OH TYR W 212 " pdb=" CE MET W 215 " model vdw 1.934 3.460 nonbonded pdb=" OG1 THR Q1178 " pdb=" CD2 LEU Q1191 " model vdw 2.041 3.460 nonbonded pdb=" CG GLN A 68 " pdb=" NE ARG A 72 " model vdw 2.272 3.520 nonbonded pdb=" N2 DG I 29 " pdb=" O2 DC J -29 " model vdw 2.276 2.496 ... (remaining 345301 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 133)) selection = (chain 'E' and (resid 41 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 133)) } ncs_group { reference = (chain 'B' and (resid 24 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 98)) selection = (chain 'F' and resid 24 through 98) } ncs_group { reference = (chain 'C' and (resid 15 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 118)) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 30 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 102 or (resid 103 through 105 and \ (name N or name CA or name C or name O or name CB )) or resid 106 through 121)) selection = (chain 'H' and resid 30 through 121) } ncs_group { reference = (chain 'T' and resid 22 through 1001) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB )) or resid 183 through 100 \ 1)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB )) or resid 183 through 100 \ 1)) } ncs_group { reference = (chain 'U' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 459 or \ resid 1001)) selection = (chain 'W' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 1001)) \ selection = (chain 'Y' and (resid 18 through 459 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.930 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 45.470 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.005 0.167 43439 Z= 0.334 Angle : 0.941 19.414 59959 Z= 0.570 Chirality : 0.054 0.526 6962 Planarity : 0.007 0.191 6690 Dihedral : 22.280 179.947 17050 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 28.77 % Favored : 71.23 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.11), residues: 4607 helix: -1.73 (0.09), residues: 2120 sheet: -0.03 (0.20), residues: 669 loop : -1.42 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 371 TYR 0.039 0.002 TYR V 323 PHE 0.055 0.002 PHE H 67 TRP 0.020 0.002 TRP Q 755 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.33 (43438) covalent geometry : angle 0.94123 / 0.57 (59959) hydrogen bonds : bond 0.15056 / 9.98 ( 1900) hydrogen bonds : angle 6.43699 / 4.55 ( 5273) Misc. bond : bond 0.00448 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.633 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: E 70 LEU cc_start: 0.8590 (pp) cc_final: 0.8260 (mp) REVERT: G 62 ILE cc_start: 0.8021 (pt) cc_final: 0.7731 (mp) REVERT: G 99 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7836 (ttp80) REVERT: H 56 MET cc_start: 0.9094 (mmm) cc_final: 0.8481 (mmp) REVERT: H 118 TYR cc_start: 0.9167 (t80) cc_final: 0.8892 (t80) REVERT: Q 786 TYR cc_start: 0.8164 (t80) cc_final: 0.7937 (t80) REVERT: Q 965 GLN cc_start: 0.8864 (mp10) cc_final: 0.8455 (pp30) REVERT: Q 1021 ASP cc_start: 0.8759 (t0) cc_final: 0.8261 (p0) REVERT: Q 1236 GLU cc_start: 0.8917 (tp30) cc_final: 0.8573 (tp30) REVERT: Q 1328 MET cc_start: 0.7560 (ttp) cc_final: 0.7051 (tmm) REVERT: R 732 LYS cc_start: 0.9340 (tptp) cc_final: 0.8777 (mmmt) REVERT: V 323 TYR cc_start: 0.8271 (t80) cc_final: 0.7973 (t80) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2594 time to fit residues: 116.5678 Evaluate side-chains 241 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 2.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Q 831 GLN Q1204 ASN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN R 132 ASN T 51 GLN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 299 HIS X 440 ASN ** Y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.099281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066194 restraints weight = 158810.806| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.47 r_work: 0.3211 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 43439 Z= 0.196 Angle : 0.638 10.976 59959 Z= 0.337 Chirality : 0.044 0.230 6962 Planarity : 0.004 0.088 6690 Dihedral : 22.610 176.150 8140 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.63 % Allowed : 25.71 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.12), residues: 4607 helix: -0.29 (0.10), residues: 2159 sheet: 0.01 (0.20), residues: 678 loop : -1.16 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 39 TYR 0.029 0.001 TYR X 462 PHE 0.027 0.001 PHE H 62 TRP 0.014 0.001 TRP Q 755 HIS 0.011 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (43438) covalent geometry : angle 0.63819 / 0.34 (59959) hydrogen bonds : bond 0.05097 / 3.39 ( 1900) hydrogen bonds : angle 4.66293 / 3.31 ( 5273) Misc. bond : bond 0.00343 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 258 time to evaluate : 1.608 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: E 70 LEU cc_start: 0.8528 (pp) cc_final: 0.8214 (mp) REVERT: Q 965 GLN cc_start: 0.8992 (mp10) cc_final: 0.8677 (pp30) REVERT: Q 1021 ASP cc_start: 0.8711 (t0) cc_final: 0.8218 (p0) REVERT: Q 1154 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: Q 1328 MET cc_start: 0.7700 (ttp) cc_final: 0.7166 (tmm) REVERT: R 165 PHE cc_start: 0.7591 (p90) cc_final: 0.7079 (p90) REVERT: R 714 MET cc_start: 0.8475 (mpp) cc_final: 0.8232 (mpp) REVERT: S 155 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7206 (t80) REVERT: T 315 MET cc_start: 0.9013 (mmm) cc_final: 0.8759 (mmm) REVERT: V 51 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8771 (mm-40) REVERT: V 323 TYR cc_start: 0.8584 (t80) cc_final: 0.8290 (t80) REVERT: W 243 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: X 268 MET cc_start: 0.8787 (mmt) cc_final: 0.8518 (mmt) outliers start: 104 outliers final: 43 residues processed: 332 average time/residue: 0.2442 time to fit residues: 139.2586 Evaluate side-chains 282 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 781 PHE Chi-restraints excluded: chain Q residue 888 MET Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1369 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 224 ASN Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 116 CYS Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 247 ILE Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 403 LEU Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 159 optimal weight: 5.9990 chunk 373 optimal weight: 5.9990 chunk 385 optimal weight: 9.9990 chunk 337 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 chunk 254 optimal weight: 0.0870 chunk 456 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 386 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Q1161 ASN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 357 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.100184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067225 restraints weight = 159034.761| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.46 r_work: 0.3238 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 43439 Z= 0.119 Angle : 0.576 11.502 59959 Z= 0.304 Chirality : 0.043 0.270 6962 Planarity : 0.004 0.073 6690 Dihedral : 22.509 179.362 8140 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.43 % Allowed : 26.37 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4607 helix: 0.34 (0.11), residues: 2161 sheet: -0.01 (0.20), residues: 681 loop : -1.03 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG G 32 TYR 0.021 0.001 TYR X 462 PHE 0.016 0.001 PHE H 62 TRP 0.011 0.001 TRP Q 755 HIS 0.010 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (43438) covalent geometry : angle 0.57633 / 0.30 (59959) hydrogen bonds : bond 0.04249 / 2.81 ( 1900) hydrogen bonds : angle 4.32824 / 3.07 ( 5273) Misc. bond : bond 0.00309 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 265 time to evaluate : 1.658 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: D 99 LEU cc_start: 0.1253 (OUTLIER) cc_final: 0.1009 (mt) REVERT: E 90 MET cc_start: 0.5525 (mpp) cc_final: 0.5191 (mpp) REVERT: G 95 LYS cc_start: 0.7839 (tppt) cc_final: 0.7631 (mmtt) REVERT: Q 786 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: Q 838 MET cc_start: 0.3705 (mtt) cc_final: 0.3330 (mtt) REVERT: Q 965 GLN cc_start: 0.8967 (mp10) cc_final: 0.8643 (pp30) REVERT: Q 1021 ASP cc_start: 0.8729 (t0) cc_final: 0.8226 (p0) REVERT: Q 1154 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: Q 1316 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6786 (t70) REVERT: R 165 PHE cc_start: 0.7545 (p90) cc_final: 0.6967 (p90) REVERT: R 714 MET cc_start: 0.8413 (mpp) cc_final: 0.8116 (mpp) REVERT: S 155 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7244 (t80) REVERT: T 422 CYS cc_start: 0.8958 (m) cc_final: 0.8595 (m) REVERT: V 51 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8734 (mm-40) REVERT: V 232 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7115 (mt) REVERT: V 323 TYR cc_start: 0.8548 (t80) cc_final: 0.8192 (t80) REVERT: W 243 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: X 268 MET cc_start: 0.8813 (mmt) cc_final: 0.8458 (mmt) REVERT: X 315 MET cc_start: 0.8962 (mmm) cc_final: 0.8456 (mmm) outliers start: 96 outliers final: 51 residues processed: 338 average time/residue: 0.2479 time to fit residues: 142.7861 Evaluate side-chains 299 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 762 THR Chi-restraints excluded: chain Q residue 781 PHE Chi-restraints excluded: chain Q residue 786 TYR Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 888 MET Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1387 ASP Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 118 THR Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 148 THR Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 232 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 403 LEU Chi-restraints excluded: chain V residue 416 LEU Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 185 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 335 THR Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 270 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 23 optimal weight: 40.0000 chunk 367 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 393 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 844 GLN Q1244 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1409 HIS R 37 GLN ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 440 ASN W 326 ASN X 190 GLN ** Y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.097674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.064446 restraints weight = 158592.121| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.41 r_work: 0.3164 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 43439 Z= 0.211 Angle : 0.633 12.242 59959 Z= 0.331 Chirality : 0.043 0.231 6962 Planarity : 0.004 0.074 6690 Dihedral : 22.490 179.850 8140 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.87 % Allowed : 25.46 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 4607 helix: 0.60 (0.11), residues: 2176 sheet: 0.02 (0.20), residues: 663 loop : -1.00 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 69 TYR 0.028 0.001 TYR X 462 PHE 0.020 0.002 PHE H 62 TRP 0.011 0.001 TRP Q 755 HIS 0.019 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (43438) covalent geometry : angle 0.63267 / 0.33 (59959) hydrogen bonds : bond 0.04671 / 3.11 ( 1900) hydrogen bonds : angle 4.24960 / 3.03 ( 5273) Misc. bond : bond 0.00403 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 257 time to evaluate : 1.602 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: G 94 ASN cc_start: 0.8146 (m-40) cc_final: 0.7810 (m110) REVERT: G 95 LYS cc_start: 0.7958 (tppt) cc_final: 0.7693 (mmtt) REVERT: Q 965 GLN cc_start: 0.8979 (mp10) cc_final: 0.8652 (pp30) REVERT: Q 1021 ASP cc_start: 0.8824 (t0) cc_final: 0.8280 (p0) REVERT: Q 1154 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: Q 1339 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: R 165 PHE cc_start: 0.7655 (p90) cc_final: 0.7121 (p90) REVERT: R 714 MET cc_start: 0.8388 (mpp) cc_final: 0.8076 (mpp) REVERT: S 155 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7712 (t80) REVERT: T 125 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8760 (m-80) REVERT: U 60 MET cc_start: 0.8160 (mmt) cc_final: 0.7571 (mtt) REVERT: U 297 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8551 (mt-10) REVERT: U 411 MET cc_start: 0.9393 (mpp) cc_final: 0.8960 (mpp) REVERT: V 232 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7244 (mt) REVERT: V 323 TYR cc_start: 0.8736 (t80) cc_final: 0.8497 (t80) REVERT: W 185 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7431 (tt) REVERT: W 243 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: W 411 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8681 (pmm) REVERT: X 268 MET cc_start: 0.8894 (mmt) cc_final: 0.8617 (mmt) REVERT: X 315 MET cc_start: 0.9034 (mmm) cc_final: 0.8355 (mmm) outliers start: 153 outliers final: 84 residues processed: 384 average time/residue: 0.2456 time to fit residues: 161.4738 Evaluate side-chains 325 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 232 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 762 THR Chi-restraints excluded: chain Q residue 786 TYR Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 888 MET Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1010 VAL Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1149 LEU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1330 LEU Chi-restraints excluded: chain Q residue 1339 GLN Chi-restraints excluded: chain Q residue 1352 GLU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 224 ASN Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 116 CYS Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 118 THR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 247 ILE Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 181 LEU Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 232 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 370 VAL Chi-restraints excluded: chain V residue 403 LEU Chi-restraints excluded: chain V residue 416 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 185 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 432 ASP Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 158 LEU Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 246 VAL Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 189 optimal weight: 7.9990 chunk 371 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 400 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 76 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 715 ASN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 HIS Y 23 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.097683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.065229 restraints weight = 156507.117| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.57 r_work: 0.3155 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 43439 Z= 0.176 Angle : 0.595 13.047 59959 Z= 0.312 Chirality : 0.043 0.242 6962 Planarity : 0.004 0.073 6690 Dihedral : 22.456 179.324 8140 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.72 % Allowed : 25.82 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.12), residues: 4607 helix: 0.79 (0.11), residues: 2173 sheet: 0.03 (0.20), residues: 659 loop : -0.99 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.026 0.001 TYR A 54 PHE 0.018 0.001 PHE H 62 TRP 0.011 0.001 TRP Q 755 HIS 0.009 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (43438) covalent geometry : angle 0.59522 / 0.31 (59959) hydrogen bonds : bond 0.04169 / 2.77 ( 1900) hydrogen bonds : angle 4.10875 / 2.94 ( 5273) Misc. bond : bond 0.00399 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 253 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 70 LEU cc_start: 0.8520 (pp) cc_final: 0.8218 (mp) REVERT: G 94 ASN cc_start: 0.8165 (m-40) cc_final: 0.7853 (m110) REVERT: G 95 LYS cc_start: 0.7984 (tppt) cc_final: 0.7724 (mmtt) REVERT: Q 838 MET cc_start: 0.3773 (mtt) cc_final: 0.3450 (mtt) REVERT: Q 965 GLN cc_start: 0.8984 (mp10) cc_final: 0.8659 (pp30) REVERT: Q 1021 ASP cc_start: 0.8889 (t0) cc_final: 0.8394 (p0) REVERT: Q 1154 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: Q 1195 LYS cc_start: 0.8893 (tppt) cc_final: 0.8530 (tmmt) REVERT: Q 1339 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: R 165 PHE cc_start: 0.7655 (p90) cc_final: 0.6939 (p90) REVERT: R 609 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8823 (pm20) REVERT: R 714 MET cc_start: 0.8335 (mpp) cc_final: 0.7698 (mtp) REVERT: S 155 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7768 (t80) REVERT: T 125 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: T 422 CYS cc_start: 0.9018 (m) cc_final: 0.8580 (m) REVERT: U 60 MET cc_start: 0.8162 (mmt) cc_final: 0.7569 (mtt) REVERT: U 166 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8677 (tm-30) REVERT: U 411 MET cc_start: 0.9413 (mpp) cc_final: 0.8916 (mpp) REVERT: V 232 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7285 (mt) REVERT: V 323 TYR cc_start: 0.8756 (t80) cc_final: 0.8538 (t80) REVERT: W 181 LYS cc_start: 0.9420 (mmtt) cc_final: 0.9110 (mmtm) REVERT: W 185 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7472 (tt) REVERT: W 243 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: W 411 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8645 (pmm) REVERT: X 268 MET cc_start: 0.8982 (mmt) cc_final: 0.8699 (mmt) REVERT: X 315 MET cc_start: 0.9029 (mmm) cc_final: 0.8474 (mmm) outliers start: 147 outliers final: 100 residues processed: 376 average time/residue: 0.2385 time to fit residues: 152.5945 Evaluate side-chains 347 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 237 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain Q residue 744 VAL Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 762 THR Chi-restraints excluded: chain Q residue 786 TYR Chi-restraints excluded: chain Q residue 807 TYR Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 888 MET Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1295 ILE Chi-restraints excluded: chain Q residue 1318 VAL Chi-restraints excluded: chain Q residue 1325 THR Chi-restraints excluded: chain Q residue 1339 GLN Chi-restraints excluded: chain Q residue 1352 GLU Chi-restraints excluded: chain Q residue 1369 VAL Chi-restraints excluded: chain Q residue 1387 ASP Chi-restraints excluded: chain Q residue 1411 LEU Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 224 ASN Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 638 ILE Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 118 THR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 225 GLU Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain U residue 23 HIS Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 220 ARG Chi-restraints excluded: chain U residue 247 ILE Chi-restraints excluded: chain U residue 370 ILE Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 181 LEU Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 232 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 403 LEU Chi-restraints excluded: chain V residue 416 LEU Chi-restraints excluded: chain V residue 439 VAL Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 88 VAL Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 185 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 424 ILE Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 158 LEU Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 309 ILE Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 383 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 338 optimal weight: 0.8980 chunk 365 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 chunk 336 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 421 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 chunk 386 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Q 715 ASN Q 874 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.098915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066014 restraints weight = 158054.863| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.48 r_work: 0.3201 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 43439 Z= 0.114 Angle : 0.568 11.381 59959 Z= 0.296 Chirality : 0.042 0.251 6962 Planarity : 0.003 0.072 6690 Dihedral : 22.369 179.186 8140 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.86 % Allowed : 26.98 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 4607 helix: 0.99 (0.11), residues: 2172 sheet: 0.06 (0.20), residues: 669 loop : -0.90 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 39 TYR 0.029 0.001 TYR A 54 PHE 0.015 0.001 PHE Q1007 TRP 0.011 0.001 TRP Q 755 HIS 0.014 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (43438) covalent geometry : angle 0.56844 / 0.30 (59959) hydrogen bonds : bond 0.03834 / 2.54 ( 1900) hydrogen bonds : angle 3.93599 / 2.82 ( 5273) Misc. bond : bond 0.00262 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 260 time to evaluate : 1.736 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: E 70 LEU cc_start: 0.8546 (pp) cc_final: 0.8230 (mp) REVERT: G 94 ASN cc_start: 0.8177 (m-40) cc_final: 0.7845 (m110) REVERT: G 95 LYS cc_start: 0.7992 (tppt) cc_final: 0.7733 (mmtt) REVERT: Q 838 MET cc_start: 0.3852 (mtt) cc_final: 0.3576 (mtt) REVERT: Q 965 GLN cc_start: 0.8951 (mp10) cc_final: 0.8638 (pp30) REVERT: Q 1021 ASP cc_start: 0.8869 (t0) cc_final: 0.8370 (p0) REVERT: Q 1154 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: Q 1195 LYS cc_start: 0.8883 (tppt) cc_final: 0.8500 (ttpt) REVERT: Q 1288 MET cc_start: 0.8656 (mmm) cc_final: 0.8431 (mmm) REVERT: Q 1316 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6720 (t70) REVERT: R 165 PHE cc_start: 0.7616 (p90) cc_final: 0.6884 (p90) REVERT: R 609 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8863 (pm20) REVERT: R 714 MET cc_start: 0.8290 (mpp) cc_final: 0.7669 (mtp) REVERT: S 155 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7782 (t80) REVERT: T 122 MET cc_start: 0.9407 (tpp) cc_final: 0.9145 (tpp) REVERT: T 125 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: T 422 CYS cc_start: 0.8977 (m) cc_final: 0.8587 (m) REVERT: U 60 MET cc_start: 0.8190 (mmt) cc_final: 0.7617 (mtt) REVERT: U 166 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8686 (tm-30) REVERT: U 297 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8495 (mt-10) REVERT: V 232 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7252 (mt) REVERT: V 323 TYR cc_start: 0.8687 (t80) cc_final: 0.8429 (t80) REVERT: W 181 LYS cc_start: 0.9349 (mmtt) cc_final: 0.9026 (mmtm) REVERT: W 185 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7420 (tt) REVERT: W 243 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: W 411 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8661 (pmm) REVERT: X 315 MET cc_start: 0.8983 (mmm) cc_final: 0.8419 (mmm) outliers start: 113 outliers final: 79 residues processed: 354 average time/residue: 0.2461 time to fit residues: 147.7103 Evaluate side-chains 334 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 244 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain Q residue 762 THR Chi-restraints excluded: chain Q residue 781 PHE Chi-restraints excluded: chain Q residue 786 TYR Chi-restraints excluded: chain Q residue 807 TYR Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 888 MET Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1325 THR Chi-restraints excluded: chain Q residue 1352 GLU Chi-restraints excluded: chain Q residue 1387 ASP Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 732 LYS Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 118 THR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 220 ARG Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 370 ILE Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 181 LEU Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 232 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 403 LEU Chi-restraints excluded: chain V residue 416 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 185 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 424 ILE Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 309 ILE Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 401 optimal weight: 0.4980 chunk 197 optimal weight: 0.9980 chunk 376 optimal weight: 0.8980 chunk 84 optimal weight: 50.0000 chunk 477 optimal weight: 5.9990 chunk 439 optimal weight: 0.6980 chunk 454 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 76 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q1279 ASN ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.099470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066597 restraints weight = 156883.204| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.47 r_work: 0.3224 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 43439 Z= 0.110 Angle : 0.562 16.081 59959 Z= 0.292 Chirality : 0.042 0.251 6962 Planarity : 0.003 0.070 6690 Dihedral : 22.288 179.139 8140 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.08 % Allowed : 26.83 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4607 helix: 1.08 (0.11), residues: 2177 sheet: 0.12 (0.20), residues: 671 loop : -0.83 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 69 TYR 0.031 0.001 TYR A 54 PHE 0.014 0.001 PHE H 67 TRP 0.010 0.001 TRP Q 755 HIS 0.010 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (43438) covalent geometry : angle 0.56193 / 0.29 (59959) hydrogen bonds : bond 0.03750 / 2.48 ( 1900) hydrogen bonds : angle 3.82887 / 2.74 ( 5273) Misc. bond : bond 0.00233 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 259 time to evaluate : 1.527 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: E 70 LEU cc_start: 0.8551 (pp) cc_final: 0.8251 (mp) REVERT: G 94 ASN cc_start: 0.8176 (m-40) cc_final: 0.7834 (m110) REVERT: G 95 LYS cc_start: 0.8029 (tppt) cc_final: 0.7777 (mmtt) REVERT: Q 838 MET cc_start: 0.3900 (mtt) cc_final: 0.3667 (mtt) REVERT: Q 965 GLN cc_start: 0.8957 (mp10) cc_final: 0.8638 (pp30) REVERT: Q 1005 MET cc_start: 0.7584 (ppp) cc_final: 0.7341 (ppp) REVERT: Q 1021 ASP cc_start: 0.8874 (t0) cc_final: 0.8374 (p0) REVERT: Q 1154 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8171 (pm20) REVERT: R 165 PHE cc_start: 0.7634 (p90) cc_final: 0.6867 (p90) REVERT: R 609 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8869 (pm20) REVERT: R 714 MET cc_start: 0.8332 (mpp) cc_final: 0.7752 (mtp) REVERT: S 154 GLU cc_start: 0.8820 (pm20) cc_final: 0.8458 (pm20) REVERT: S 155 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7865 (t80) REVERT: T 122 MET cc_start: 0.9460 (tpp) cc_final: 0.9209 (tpp) REVERT: T 125 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: T 422 CYS cc_start: 0.8963 (m) cc_final: 0.8614 (m) REVERT: U 60 MET cc_start: 0.8188 (mmt) cc_final: 0.7627 (mtt) REVERT: U 166 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8667 (tm-30) REVERT: U 297 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8485 (mt-10) REVERT: U 411 MET cc_start: 0.9366 (mpp) cc_final: 0.8969 (mpp) REVERT: V 232 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7231 (mt) REVERT: V 323 TYR cc_start: 0.8683 (t80) cc_final: 0.8411 (t80) REVERT: W 181 LYS cc_start: 0.9329 (mmtt) cc_final: 0.8937 (tppt) REVERT: W 182 GLU cc_start: 0.9014 (mp0) cc_final: 0.8802 (mp0) REVERT: W 185 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7398 (tt) REVERT: W 243 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: W 411 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8658 (pmm) REVERT: X 268 MET cc_start: 0.8893 (mmt) cc_final: 0.8556 (mmt) REVERT: X 315 MET cc_start: 0.8974 (mmm) cc_final: 0.8455 (mmm) outliers start: 122 outliers final: 88 residues processed: 358 average time/residue: 0.2346 time to fit residues: 143.2430 Evaluate side-chains 344 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 246 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain Q residue 744 VAL Chi-restraints excluded: chain Q residue 762 THR Chi-restraints excluded: chain Q residue 781 PHE Chi-restraints excluded: chain Q residue 786 TYR Chi-restraints excluded: chain Q residue 807 TYR Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 888 MET Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1318 VAL Chi-restraints excluded: chain Q residue 1325 THR Chi-restraints excluded: chain Q residue 1352 GLU Chi-restraints excluded: chain Q residue 1369 VAL Chi-restraints excluded: chain Q residue 1411 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 118 THR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 220 ARG Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 370 ILE Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 181 LEU Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 232 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 403 LEU Chi-restraints excluded: chain V residue 416 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 88 VAL Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 185 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 424 ILE Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 158 LEU Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 309 ILE Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 53 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 389 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 133 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 429 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 715 ASN Q 769 ASN ** Q1341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1444 GLN R 745 HIS ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN X 314 ASN ** Y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.096285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.063376 restraints weight = 157272.661| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.29 r_work: 0.3140 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 43439 Z= 0.248 Angle : 0.667 14.397 59959 Z= 0.343 Chirality : 0.045 0.362 6962 Planarity : 0.004 0.068 6690 Dihedral : 22.378 179.075 8140 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.64 % Allowed : 26.52 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.13), residues: 4607 helix: 0.91 (0.11), residues: 2174 sheet: 0.04 (0.20), residues: 672 loop : -0.94 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 76 TYR 0.030 0.002 TYR X 462 PHE 0.016 0.002 PHE H 62 TRP 0.010 0.002 TRP Q 755 HIS 0.018 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.25 (43438) covalent geometry : angle 0.66737 / 0.34 (59959) hydrogen bonds : bond 0.04707 / 3.14 ( 1900) hydrogen bonds : angle 4.09435 / 2.93 ( 5273) Misc. bond : bond 0.00399 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 249 time to evaluate : 1.577 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: D 59 MET cc_start: 0.7766 (mtp) cc_final: 0.7543 (tmm) REVERT: E 70 LEU cc_start: 0.8533 (pp) cc_final: 0.8264 (mp) REVERT: F 81 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7429 (p) REVERT: H 117 LYS cc_start: 0.9715 (mmtt) cc_final: 0.9505 (tptt) REVERT: H 118 TYR cc_start: 0.9135 (t80) cc_final: 0.8801 (t80) REVERT: Q 965 GLN cc_start: 0.8998 (mp10) cc_final: 0.8682 (pp30) REVERT: Q 1021 ASP cc_start: 0.8969 (t0) cc_final: 0.8442 (p0) REVERT: Q 1154 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: Q 1195 LYS cc_start: 0.8855 (tppt) cc_final: 0.8471 (tmmt) REVERT: Q 1316 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6863 (t70) REVERT: R 165 PHE cc_start: 0.7855 (p90) cc_final: 0.7155 (p90) REVERT: R 609 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8750 (pm20) REVERT: R 714 MET cc_start: 0.8594 (mpp) cc_final: 0.8078 (mtp) REVERT: S 154 GLU cc_start: 0.8856 (pm20) cc_final: 0.8603 (pm20) REVERT: S 155 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8137 (t80) REVERT: T 125 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8845 (m-80) REVERT: T 422 CYS cc_start: 0.9014 (m) cc_final: 0.8512 (m) REVERT: U 60 MET cc_start: 0.8371 (mmt) cc_final: 0.7853 (mtt) REVERT: U 166 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8697 (tm-30) REVERT: V 51 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.7913 (mm-40) REVERT: V 232 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7381 (mt) REVERT: W 181 LYS cc_start: 0.9378 (mmtt) cc_final: 0.9144 (mmtp) REVERT: W 185 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7531 (tt) REVERT: W 243 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: W 411 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8660 (pmm) REVERT: X 311 ASP cc_start: 0.8305 (t0) cc_final: 0.8012 (t0) REVERT: X 315 MET cc_start: 0.9068 (mmm) cc_final: 0.8555 (mmm) outliers start: 144 outliers final: 107 residues processed: 372 average time/residue: 0.2492 time to fit residues: 156.5310 Evaluate side-chains 355 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 236 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain Q residue 744 VAL Chi-restraints excluded: chain Q residue 761 VAL Chi-restraints excluded: chain Q residue 762 THR Chi-restraints excluded: chain Q residue 786 TYR Chi-restraints excluded: chain Q residue 807 TYR Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 888 MET Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1010 VAL Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1149 LEU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1271 THR Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1318 VAL Chi-restraints excluded: chain Q residue 1325 THR Chi-restraints excluded: chain Q residue 1330 LEU Chi-restraints excluded: chain Q residue 1352 GLU Chi-restraints excluded: chain Q residue 1369 VAL Chi-restraints excluded: chain Q residue 1387 ASP Chi-restraints excluded: chain Q residue 1411 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 224 ASN Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 118 THR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 225 GLU Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 44 MET Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 370 ILE Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 181 LEU Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 232 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 403 LEU Chi-restraints excluded: chain V residue 416 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 88 VAL Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 168 ILE Chi-restraints excluded: chain W residue 185 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 424 ILE Chi-restraints excluded: chain X residue 456 LEU Chi-restraints excluded: chain Y residue 72 LEU Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 158 LEU Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 309 ILE Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 419 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 279 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 482 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 715 ASN ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.098456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.065400 restraints weight = 157170.385| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.45 r_work: 0.3194 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43439 Z= 0.120 Angle : 0.592 13.094 59959 Z= 0.304 Chirality : 0.043 0.353 6962 Planarity : 0.003 0.070 6690 Dihedral : 22.326 179.296 8140 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.83 % Allowed : 27.33 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 4607 helix: 1.12 (0.11), residues: 2169 sheet: 0.09 (0.20), residues: 661 loop : -0.84 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.000 ARG H 69 TYR 0.031 0.001 TYR A 54 PHE 0.012 0.001 PHE Q1007 TRP 0.010 0.001 TRP Q 755 HIS 0.011 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (43438) covalent geometry : angle 0.59184 / 0.30 (59959) hydrogen bonds : bond 0.03828 / 2.53 ( 1900) hydrogen bonds : angle 3.90353 / 2.79 ( 5273) Misc. bond : bond 0.00283 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 255 time to evaluate : 1.773 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: E 70 LEU cc_start: 0.8540 (pp) cc_final: 0.8257 (mp) REVERT: G 94 ASN cc_start: 0.8253 (m-40) cc_final: 0.7923 (m110) REVERT: G 95 LYS cc_start: 0.8084 (tppt) cc_final: 0.7831 (mmtt) REVERT: H 118 TYR cc_start: 0.9135 (t80) cc_final: 0.8851 (t80) REVERT: Q 838 MET cc_start: 0.4204 (mtt) cc_final: 0.3891 (mtt) REVERT: Q 965 GLN cc_start: 0.9007 (mp10) cc_final: 0.8678 (pp30) REVERT: Q 1021 ASP cc_start: 0.8923 (t0) cc_final: 0.8460 (p0) REVERT: Q 1316 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6787 (t70) REVERT: R 165 PHE cc_start: 0.7812 (p90) cc_final: 0.6966 (p90) REVERT: R 609 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: R 714 MET cc_start: 0.8563 (mpp) cc_final: 0.7983 (mtp) REVERT: S 154 GLU cc_start: 0.8842 (pm20) cc_final: 0.8547 (pm20) REVERT: S 155 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8036 (t80) REVERT: T 122 MET cc_start: 0.9457 (tpp) cc_final: 0.9190 (tpp) REVERT: T 125 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8619 (m-80) REVERT: T 422 CYS cc_start: 0.8986 (m) cc_final: 0.8586 (m) REVERT: U 166 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8703 (tm-30) REVERT: U 297 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: V 232 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7312 (mt) REVERT: W 181 LYS cc_start: 0.9326 (mmtt) cc_final: 0.9042 (mmtp) REVERT: W 185 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7531 (tt) REVERT: W 243 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: W 411 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8645 (pmm) REVERT: X 268 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8648 (mmt) REVERT: X 315 MET cc_start: 0.9000 (mmm) cc_final: 0.8463 (mmm) outliers start: 112 outliers final: 94 residues processed: 350 average time/residue: 0.2415 time to fit residues: 143.9808 Evaluate side-chains 352 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 247 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain Q residue 744 VAL Chi-restraints excluded: chain Q residue 762 THR Chi-restraints excluded: chain Q residue 781 PHE Chi-restraints excluded: chain Q residue 786 TYR Chi-restraints excluded: chain Q residue 807 TYR Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 888 MET Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1010 VAL Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1295 ILE Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1318 VAL Chi-restraints excluded: chain Q residue 1352 GLU Chi-restraints excluded: chain Q residue 1369 VAL Chi-restraints excluded: chain Q residue 1387 ASP Chi-restraints excluded: chain Q residue 1411 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 71 ARG Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 118 THR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 370 ILE Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 181 LEU Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 232 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 403 LEU Chi-restraints excluded: chain V residue 416 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 88 VAL Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 185 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 243 GLU Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 424 ILE Chi-restraints excluded: chain X residue 456 LEU Chi-restraints excluded: chain Y residue 72 LEU Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 309 ILE Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Z residue 309 LEU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 202 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 336 optimal weight: 4.9990 chunk 457 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 453 optimal weight: 0.5980 chunk 414 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 chunk 433 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.099149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066111 restraints weight = 157509.428| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.44 r_work: 0.3214 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 43439 Z= 0.112 Angle : 0.587 13.446 59959 Z= 0.302 Chirality : 0.042 0.355 6962 Planarity : 0.003 0.071 6690 Dihedral : 22.227 179.735 8140 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.60 % Allowed : 27.61 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4607 helix: 1.18 (0.11), residues: 2170 sheet: 0.17 (0.21), residues: 662 loop : -0.76 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 69 TYR 0.031 0.001 TYR A 54 PHE 0.020 0.001 PHE D 67 TRP 0.012 0.001 TRP R 108 HIS 0.011 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (43438) covalent geometry : angle 0.58748 / 0.30 (59959) hydrogen bonds : bond 0.03762 / 2.48 ( 1900) hydrogen bonds : angle 3.82558 / 2.72 ( 5273) Misc. bond : bond 0.00242 / 0.13 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9214 Ramachandran restraints generated. 4607 Oldfield, 0 Emsley, 4607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 260 time to evaluate : 1.446 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: E 70 LEU cc_start: 0.8534 (pp) cc_final: 0.8280 (mp) REVERT: H 117 LYS cc_start: 0.9660 (mmtt) cc_final: 0.9457 (tttt) REVERT: H 118 TYR cc_start: 0.9113 (t80) cc_final: 0.8810 (t80) REVERT: Q 838 MET cc_start: 0.4355 (mtt) cc_final: 0.4060 (mtt) REVERT: Q 965 GLN cc_start: 0.9001 (mp10) cc_final: 0.8686 (pp30) REVERT: Q 1005 MET cc_start: 0.7650 (ppp) cc_final: 0.7277 (ppp) REVERT: Q 1021 ASP cc_start: 0.8893 (t0) cc_final: 0.8506 (p0) REVERT: Q 1316 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6712 (t70) REVERT: R 165 PHE cc_start: 0.7831 (p90) cc_final: 0.7006 (p90) REVERT: R 609 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8893 (pm20) REVERT: R 714 MET cc_start: 0.8537 (mpp) cc_final: 0.7955 (mtp) REVERT: S 154 GLU cc_start: 0.8807 (pm20) cc_final: 0.8506 (pm20) REVERT: S 155 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7988 (t80) REVERT: T 122 MET cc_start: 0.9454 (tpp) cc_final: 0.9218 (tpp) REVERT: T 125 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8639 (m-80) REVERT: T 422 CYS cc_start: 0.8971 (m) cc_final: 0.8588 (m) REVERT: U 166 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8670 (tm-30) REVERT: U 276 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8548 (ttmm) REVERT: U 297 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: V 232 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7289 (mt) REVERT: W 181 LYS cc_start: 0.9302 (mmtt) cc_final: 0.9054 (tptt) REVERT: W 185 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7552 (tt) REVERT: W 323 MET cc_start: 0.8822 (mtm) cc_final: 0.8568 (ptp) REVERT: W 411 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8673 (pmm) REVERT: X 268 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8623 (mmt) REVERT: X 315 MET cc_start: 0.8969 (mmm) cc_final: 0.8462 (mmm) outliers start: 103 outliers final: 85 residues processed: 348 average time/residue: 0.2428 time to fit residues: 145.0625 Evaluate side-chains 347 residues out of total 4020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 251 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain Q residue 762 THR Chi-restraints excluded: chain Q residue 781 PHE Chi-restraints excluded: chain Q residue 807 TYR Chi-restraints excluded: chain Q residue 871 THR Chi-restraints excluded: chain Q residue 888 MET Chi-restraints excluded: chain Q residue 901 TRP Chi-restraints excluded: chain Q residue 1010 VAL Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1295 ILE Chi-restraints excluded: chain Q residue 1316 HIS Chi-restraints excluded: chain Q residue 1318 VAL Chi-restraints excluded: chain Q residue 1352 GLU Chi-restraints excluded: chain Q residue 1369 VAL Chi-restraints excluded: chain Q residue 1387 ASP Chi-restraints excluded: chain Q residue 1411 LEU Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 224 ASN Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 155 TYR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 118 THR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 254 VAL Chi-restraints excluded: chain T residue 331 ASN Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 189 VAL Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 276 LYS Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 370 ILE Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 181 LEU Chi-restraints excluded: chain V residue 206 THR Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 232 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 403 LEU Chi-restraints excluded: chain V residue 416 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain W residue 88 VAL Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 185 LEU Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 424 ILE Chi-restraints excluded: chain X residue 456 LEU Chi-restraints excluded: chain Y residue 104 SER Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 309 ILE Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Z residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 485 random chunks: chunk 465 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 405 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 151 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 80 optimal weight: 50.0000 chunk 415 optimal weight: 6.9990 chunk 88 optimal weight: 50.0000 overall best weight: 2.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.097787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.064718 restraints weight = 158006.679| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.38 r_work: 0.3182 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 43439 Z= 0.172 Angle : 0.610 13.057 59959 Z= 0.313 Chirality : 0.043 0.390 6962 Planarity : 0.003 0.070 6690 Dihedral : 22.239 179.772 8140 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.65 % Allowed : 27.71 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 4607 helix: 1.16 (0.11), residues: 2170 sheet: 0.11 (0.21), residues: 653 loop : -0.80 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 69 TYR 0.033 0.001 TYR A 54 PHE 0.016 0.001 PHE H 62 TRP 0.010 0.001 TRP Q 755 HIS 0.009 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (43438) covalent geometry : angle 0.61034 / 0.31 (59959) hydrogen bonds : bond 0.04041 / 2.68 ( 1900) hydrogen bonds : angle 3.88867 / 2.77 ( 5273) Misc. bond : bond 0.00316 / 0.17 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13418.70 seconds wall clock time: 229 minutes 52.71 seconds (13792.71 seconds total)