Starting phenix.real_space_refine on Tue Sep 15 13:46:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6eu1_3956/09_2026/6eu1_3956_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eu1_3956/09_2026/6eu1_3956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6eu1_3956/09_2026/6eu1_3956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eu1_3956/09_2026/6eu1_3956.map" model { file = "/net/cci-nas-00/data/ceres_data/6eu1_3956/09_2026/6eu1_3956_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eu1_3956/09_2026/6eu1_3956_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 43 5.49 5 Mg 1 5.21 5 S 208 5.16 5 C 25531 2.51 5 N 7000 2.21 5 O 7758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40547 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1433, 11187 Classifications: {'peptide': 1433} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 66, 'TRANS': 1366} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 42, 'TRANS': 1069} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 312} Chain: "D" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1070 Classifications: {'peptide': 138} Incomplete info: {'backbone_only': 17} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1690 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 195} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1161 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "I" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 341 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} 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: "L" Number of atoms: 366 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Conformer: "B" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} bond proxies already assigned to first conformer: 351 Chain: "M" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1402 Classifications: {'peptide': 172} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 162} Chain breaks: 1 Chain: "N" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 864 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4426 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain breaks: 1 Chain: "P" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1210 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "Q" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 707 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain: "R" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "S" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 557 SG CYS A 77 81.816 64.151 80.878 1.00 23.93 S ATOM 795 SG CYS A 107 65.427 111.466 94.677 1.00 15.86 S ATOM 19657 SG CYS B1110 80.756 83.664 72.428 1.00 22.87 S ATOM 29020 SG CYS I 5 67.200 108.248 159.384 1.00 34.15 S ATOM 29685 SG CYS J 46 131.983 38.091 128.039 1.00 5.89 S ATOM 30736 SG CYS L 31 87.696 25.579 122.308 1.00 10.62 S ATOM 30868 SG CYS L 48 85.442 22.403 121.836 1.00 16.88 S ATOM 30891 SG CYS L 51 84.177 24.264 125.447 1.00 16.50 S Time building chain proxies: 8.26, per 1000 atoms: 0.20 Number of scatterers: 40547 At special positions: 0 Unit cell: (190.05, 157.5, 205.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 208 16.00 P 43 15.00 Mg 1 11.99 O 7758 8.00 N 7000 7.00 C 25531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9426 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 45 sheets defined 31.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.964A pdb=" N GLN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.714A pdb=" N ARG A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.518A pdb=" N LEU A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 4.088A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 4.194A pdb=" N LEU A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 223 through 232 removed outlier: 4.507A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.632A pdb=" N VAL A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.987A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.657A pdb=" N ILE A 558 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 559' Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.523A pdb=" N GLN A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.691A pdb=" N LEU A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 685 Processing helix chain 'A' and resid 685 through 709 removed outlier: 4.111A pdb=" N GLU A 689 " --> pdb=" O TYR A 685 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 698 " --> pdb=" O MET A 694 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 747 removed outlier: 4.986A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.857A pdb=" N ALA A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 775 " --> pdb=" O SER A 771 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 809 removed outlier: 3.655A pdb=" N MET A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 871 removed outlier: 3.764A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 870 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 892 removed outlier: 4.027A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.841A pdb=" N ASP A 940 " --> pdb=" O ASN A 936 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 963 removed outlier: 3.602A pdb=" N GLU A 961 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1026 removed outlier: 3.597A pdb=" N PHE A1004 " --> pdb=" O ALA A1000 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1060 removed outlier: 3.661A pdb=" N VAL A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1080 removed outlier: 3.737A pdb=" N LEU A1071 " --> pdb=" O VAL A1067 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1095 removed outlier: 3.748A pdb=" N GLN A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 3.624A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 4.087A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1211 removed outlier: 3.663A pdb=" N ILE A1209 " --> pdb=" O ILE A1205 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1244 Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 3.837A pdb=" N ASN A1254 " --> pdb=" O PRO A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1266 removed outlier: 3.533A pdb=" N ARG A1265 " --> pdb=" O GLN A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.545A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.821A pdb=" N TYR A1333 " --> pdb=" O GLU A1329 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A1344 " --> pdb=" O ASN A1340 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1359 removed outlier: 3.706A pdb=" N LEU A1357 " --> pdb=" O ARG A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1387 removed outlier: 3.632A pdb=" N LEU A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1402 removed outlier: 4.077A pdb=" N LEU A1396 " --> pdb=" O THR A1392 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A1401 " --> pdb=" O PHE A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1427 removed outlier: 3.819A pdb=" N SER A1427 " --> pdb=" O GLY A1424 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.568A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.376A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.558A pdb=" N LEU B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 121' Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.809A pdb=" N VAL B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.581A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 354 through 362 removed outlier: 4.318A pdb=" N MET B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 405 removed outlier: 4.198A pdb=" N LEU B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 437 removed outlier: 3.800A pdb=" N GLY B 432 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.561A pdb=" N LYS B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.562A pdb=" N GLN B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.794A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.764A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 642' Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.754A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 707 removed outlier: 3.882A pdb=" N ASN B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 704 " --> pdb=" O THR B 700 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 779 Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.608A pdb=" N GLY B 948 " --> pdb=" O ASN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 971 removed outlier: 4.732A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 995 removed outlier: 3.948A pdb=" N LEU B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1035 Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 3.616A pdb=" N ASP B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B1072 " --> pdb=" O ASP B1068 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B1073 " --> pdb=" O CYS B1069 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B1074 " --> pdb=" O VAL B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1082 removed outlier: 3.797A pdb=" N LEU B1080 " --> pdb=" O SER B1076 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B1081 " --> pdb=" O GLN B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1136 removed outlier: 3.587A pdb=" N SER B1134 " --> pdb=" O GLN B1130 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET B1135 " --> pdb=" O GLU B1131 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B1136 " --> pdb=" O LEU B1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.512A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 removed outlier: 3.564A pdb=" N ILE C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 removed outlier: 4.135A pdb=" N LYS C 125 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.579A pdb=" N ASP C 166 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.616A pdb=" N SER C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.739A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.952A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.717A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.732A pdb=" N LEU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 37 removed outlier: 3.760A pdb=" N ALA D 36 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU D 37 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 removed outlier: 3.742A pdb=" N GLY D 57 " --> pdb=" O PRO D 53 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 110 through 113 removed outlier: 3.759A pdb=" N PHE D 113 " --> pdb=" O LEU D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 113' Processing helix chain 'D' and resid 116 through 126 removed outlier: 3.615A pdb=" N GLN D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 removed outlier: 4.028A pdb=" N LEU D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 3.973A pdb=" N ILE D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.501A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.882A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.838A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.908A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET E 58 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 58' Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 119 through 123 removed outlier: 4.020A pdb=" N LYS E 122 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU E 123 " --> pdb=" O ALA E 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 119 through 123' Processing helix chain 'E' and resid 137 through 141 removed outlier: 4.074A pdb=" N LEU E 140 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 141' Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.711A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 87 through 103 removed outlier: 3.520A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 162 through 167 Processing helix chain 'G' and resid 168 through 175 Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.676A pdb=" N LEU J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 removed outlier: 3.655A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 48 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.579A pdb=" N LEU J 61 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG J 62 " --> pdb=" O LYS J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.727A pdb=" N ASN K 74 " --> pdb=" O HIS K 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 137 removed outlier: 3.567A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 100 removed outlier: 3.859A pdb=" N LYS M 100 " --> pdb=" O VAL M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 197 removed outlier: 4.623A pdb=" N VAL M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS M 194 " --> pdb=" O ASN M 190 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN M 195 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 262 removed outlier: 4.076A pdb=" N LYS M 261 " --> pdb=" O ASP M 257 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU M 262 " --> pdb=" O THR M 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 286 Processing helix chain 'N' and resid 288 through 296 removed outlier: 3.565A pdb=" N LYS N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 55 removed outlier: 3.630A pdb=" N TYR O 49 " --> pdb=" O ASP O 45 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 69 removed outlier: 4.851A pdb=" N VAL O 64 " --> pdb=" O ARG O 60 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 84 removed outlier: 3.831A pdb=" N ILE O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 79 through 84' Processing helix chain 'O' and resid 87 through 92 removed outlier: 3.620A pdb=" N VAL O 91 " --> pdb=" O ASP O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 124 through 144 removed outlier: 5.111A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU O 131 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR O 142 " --> pdb=" O ASP O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 166 removed outlier: 3.942A pdb=" N GLN O 154 " --> pdb=" O GLU O 150 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN O 161 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN O 162 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU O 166 " --> pdb=" O ASN O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 178 removed outlier: 3.659A pdb=" N SER O 177 " --> pdb=" O TYR O 174 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL O 178 " --> pdb=" O LEU O 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 174 through 178' Processing helix chain 'O' and resid 182 through 196 removed outlier: 3.857A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 removed outlier: 3.741A pdb=" N HIS O 207 " --> pdb=" O SER O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 224 removed outlier: 3.849A pdb=" N TRP O 215 " --> pdb=" O ILE O 211 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN O 216 " --> pdb=" O GLU O 212 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS O 221 " --> pdb=" O PHE O 217 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 254 removed outlier: 3.702A pdb=" N MET O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE O 252 " --> pdb=" O ASP O 248 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN O 254 " --> pdb=" O ALA O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 258 removed outlier: 3.649A pdb=" N GLU O 258 " --> pdb=" O LYS O 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 255 through 258' Processing helix chain 'O' and resid 285 through 304 removed outlier: 4.053A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 315 removed outlier: 3.966A pdb=" N VAL O 311 " --> pdb=" O VAL O 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 341 through 353 Processing helix chain 'O' and resid 458 through 464 removed outlier: 4.215A pdb=" N ASN O 464 " --> pdb=" O ALA O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 501 removed outlier: 4.035A pdb=" N SER O 489 " --> pdb=" O PRO O 485 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU O 493 " --> pdb=" O SER O 489 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR O 494 " --> pdb=" O SER O 490 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER O 498 " --> pdb=" O TYR O 494 " (cutoff:3.500A) Processing helix chain 'O' and resid 503 through 509 removed outlier: 3.616A pdb=" N LEU O 507 " --> pdb=" O SER O 503 " (cutoff:3.500A) Processing helix chain 'O' and resid 509 through 514 removed outlier: 3.504A pdb=" N ASP O 513 " --> pdb=" O ARG O 509 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 524 removed outlier: 3.598A pdb=" N SER O 524 " --> pdb=" O LYS O 520 " (cutoff:3.500A) Processing helix chain 'O' and resid 531 through 539 removed outlier: 3.901A pdb=" N THR O 536 " --> pdb=" O ASP O 532 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU O 537 " --> pdb=" O ILE O 533 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 599 removed outlier: 4.048A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR O 574 " --> pdb=" O GLU O 570 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN O 575 " --> pdb=" O THR O 571 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN O 599 " --> pdb=" O LEU O 595 " (cutoff:3.500A) Processing helix chain 'O' and resid 623 through 627 Processing helix chain 'O' and resid 632 through 649 removed outlier: 3.656A pdb=" N PHE O 638 " --> pdb=" O GLU O 634 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU O 647 " --> pdb=" O ARG O 643 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU O 649 " --> pdb=" O LEU O 645 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 191 removed outlier: 4.026A pdb=" N THR P 180 " --> pdb=" O ASN P 176 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL P 182 " --> pdb=" O LEU P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 198 removed outlier: 3.994A pdb=" N ASN P 197 " --> pdb=" O ASN P 193 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE P 198 " --> pdb=" O GLY P 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 193 through 198' Processing helix chain 'P' and resid 202 through 209 removed outlier: 4.525A pdb=" N VAL P 206 " --> pdb=" O PRO P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 227 Processing helix chain 'P' and resid 239 through 248 removed outlier: 3.702A pdb=" N LEU P 243 " --> pdb=" O ASN P 239 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS P 244 " --> pdb=" O ILE P 240 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU P 245 " --> pdb=" O ARG P 241 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL P 248 " --> pdb=" O CYS P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 270 removed outlier: 4.077A pdb=" N LEU P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 65 removed outlier: 3.722A pdb=" N ARG Q 52 " --> pdb=" O THR Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 68 No H-bonds generated for 'chain 'Q' and resid 66 through 68' Processing helix chain 'Q' and resid 83 through 88 Processing helix chain 'Q' and resid 101 through 116 removed outlier: 4.270A pdb=" N GLU Q 106 " --> pdb=" O ASN Q 102 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG Q 107 " --> pdb=" O ASP Q 103 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER Q 109 " --> pdb=" O ILE Q 105 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP Q 110 " --> pdb=" O GLU Q 106 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS Q 111 " --> pdb=" O ARG Q 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR Q 112 " --> pdb=" O TYR Q 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU Q 113 " --> pdb=" O SER Q 109 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS Q 114 " --> pdb=" O ASP Q 110 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 4.924A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 7.053A pdb=" N VAL A 32 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N LYS A 85 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 86 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N LEU A 88 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N ILE A 257 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.747A pdb=" N HIS A 180 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 220 " --> pdb=" O HIS A 180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 498 through 500 removed outlier: 7.699A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 498 through 500 removed outlier: 7.699A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.646A pdb=" N VAL A 394 " --> pdb=" O ARG A 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 403 through 405 removed outlier: 6.990A pdb=" N GLU A 463 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 475 Processing sheet with id=AB1, first strand: chain 'A' and resid 625 through 628 removed outlier: 6.373A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.451A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 912 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1280 through 1285 removed outlier: 3.633A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A1143 " --> pdb=" O LEU A1293 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.848A pdb=" N LYS A1429 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 95 through 100 removed outlier: 5.039A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP B 132 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 129 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.542A pdb=" N THR B 190 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 197 through 198 Processing sheet with id=AB8, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AB9, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AC1, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.637A pdb=" N GLU B 786 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 904 " --> pdb=" O CYS B 785 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AC3, first strand: chain 'B' and resid 925 through 926 removed outlier: 6.340A pdb=" N LEU B 773 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE B 942 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B1017 " --> pdb=" O ASP B1002 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 793 through 794 Processing sheet with id=AC5, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AC6, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 4.201A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B1094 " --> pdb=" O ILE B1117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 12 through 13 removed outlier: 4.463A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 55 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 12 through 13 removed outlier: 4.463A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 290 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.526A pdb=" N ILE C 202 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.693A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.818A pdb=" N GLY C 257 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 266 " --> pdb=" O GLY C 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.449A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 4 removed outlier: 3.552A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 4 removed outlier: 8.425A pdb=" N ASN G 69 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU G 52 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASP G 50 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 108 through 110 removed outlier: 8.165A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER G 90 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE G 146 " --> pdb=" O GLY G 87 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.682A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP H 53 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AE1, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.503A pdb=" N LEU H 143 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR H 95 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 100 through 103 removed outlier: 5.989A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 60 through 64 removed outlier: 6.595A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 85 through 87 Processing sheet with id=AE5, first strand: chain 'M' and resid 122 through 124 Processing sheet with id=AE6, first strand: chain 'N' and resid 306 through 308 removed outlier: 6.316A pdb=" N VAL N 306 " --> pdb=" O ILE N 416 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'N' and resid 365 through 366 Processing sheet with id=AE8, first strand: chain 'O' and resid 109 through 110 removed outlier: 4.100A pdb=" N GLU O 109 " --> pdb=" O THR O 117 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 548 through 549 removed outlier: 3.709A pdb=" N GLN O 549 " --> pdb=" O LEU O 565 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU O 565 " --> pdb=" O GLN O 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 915 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.49 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12630 1.34 - 1.46: 7654 1.46 - 1.58: 20652 1.58 - 1.70: 87 1.70 - 1.82: 338 Bond restraints: 41361 Sorted by residual: bond pdb=" CA GLU E 36 " pdb=" CB GLU E 36 " ideal model delta sigma weight residual 1.526 1.611 -0.085 1.51e-02 4.39e+03 3.18e+01 bond pdb=" C LYS O 255 " pdb=" N PRO O 256 " ideal model delta sigma weight residual 1.337 1.378 -0.042 9.80e-03 1.04e+04 1.80e+01 bond pdb=" C LYS A 599 " pdb=" N PRO A 600 " ideal model delta sigma weight residual 1.332 1.375 -0.043 1.12e-02 7.97e+03 1.47e+01 bond pdb=" C1' DT R 52 " pdb=" N1 DT R 52 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.34e+01 bond pdb=" C VAL A1442 " pdb=" N PRO A1443 " ideal model delta sigma weight residual 1.334 1.373 -0.039 1.11e-02 8.12e+03 1.26e+01 ... (remaining 41356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 55110 3.76 - 7.52: 784 7.52 - 11.29: 129 11.29 - 15.05: 12 15.05 - 18.81: 1 Bond angle restraints: 56036 Sorted by residual: angle pdb=" C LYS A 666 " pdb=" N SER A 667 " pdb=" CA SER A 667 " ideal model delta sigma weight residual 121.54 134.62 -13.08 1.91e+00 2.74e-01 4.69e+01 angle pdb=" C MET A 274 " pdb=" N GLN A 275 " pdb=" CA GLN A 275 " ideal model delta sigma weight residual 122.36 132.28 -9.92 1.47e+00 4.63e-01 4.55e+01 angle pdb=" N PRO A 349 " pdb=" CA PRO A 349 " pdb=" CB PRO A 349 " ideal model delta sigma weight residual 103.25 110.24 -6.99 1.05e+00 9.07e-01 4.43e+01 angle pdb=" N ILE P 240 " pdb=" CA ILE P 240 " pdb=" C ILE P 240 " ideal model delta sigma weight residual 112.83 106.45 6.38 9.90e-01 1.02e+00 4.15e+01 angle pdb=" C LYS A 348 " pdb=" N PRO A 349 " pdb=" CA PRO A 349 " ideal model delta sigma weight residual 119.84 127.47 -7.63 1.25e+00 6.40e-01 3.73e+01 ... (remaining 56031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 23113 16.12 - 32.25: 1499 32.25 - 48.37: 504 48.37 - 64.50: 113 64.50 - 80.62: 33 Dihedral angle restraints: 25262 sinusoidal: 10673 harmonic: 14589 Sorted by residual: dihedral pdb=" CA SER M 116 " pdb=" C SER M 116 " pdb=" N HIS M 117 " pdb=" CA HIS M 117 " ideal model delta harmonic sigma weight residual -180.00 -118.18 -61.82 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ASN P 205 " pdb=" C ASN P 205 " pdb=" N VAL P 206 " pdb=" CA VAL P 206 " ideal model delta harmonic sigma weight residual -180.00 -119.48 -60.52 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ASP C 128 " pdb=" C ASP C 128 " pdb=" N GLU C 129 " pdb=" CA GLU C 129 " ideal model delta harmonic sigma weight residual -180.00 -125.75 -54.25 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 25259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 5237 0.078 - 0.156: 915 0.156 - 0.235: 131 0.235 - 0.313: 23 0.313 - 0.391: 6 Chirality restraints: 6312 Sorted by residual: chirality pdb=" CB ILE A 13 " pdb=" CA ILE A 13 " pdb=" CG1 ILE A 13 " pdb=" CG2 ILE A 13 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CB ILE B 843 " pdb=" CA ILE B 843 " pdb=" CG1 ILE B 843 " pdb=" CG2 ILE B 843 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE M 173 " pdb=" CA ILE M 173 " pdb=" CG1 ILE M 173 " pdb=" CG2 ILE M 173 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 6309 not shown) Planarity restraints: 7090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1267 " 0.059 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO A1268 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A1268 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1268 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 45 " 0.057 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO Q 46 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO Q 46 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO Q 46 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN O 43 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO O 44 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO O 44 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO O 44 " -0.045 5.00e-02 4.00e+02 ... (remaining 7087 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 31 2.37 - 3.00: 18614 3.00 - 3.63: 58493 3.63 - 4.27: 86439 4.27 - 4.90: 140995 Nonbonded interactions: 304572 Sorted by model distance: nonbonded pdb=" CD1 ILE M 71 " pdb=" CD LYS N 367 " model vdw 1.732 3.860 nonbonded pdb=" O LEU M 76 " pdb=" O VAL N 360 " model vdw 1.899 3.040 nonbonded pdb=" O LYS M 164 " pdb=" N MET M 166 " model vdw 2.124 3.120 nonbonded pdb=" NH2 ARG N 364 " pdb=" CG LYS N 374 " model vdw 2.139 3.520 nonbonded pdb=" CE2 PHE M 74 " pdb=" CD2 LEU N 294 " model vdw 2.157 3.760 ... (remaining 304567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 41.650 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0063 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 : 0.007 0.696 41369 Z= 0.318 Angle : 1.141 18.809 56036 Z= 0.608 Chirality : 0.063 0.391 6312 Planarity : 0.008 0.090 7090 Dihedral : 13.016 80.624 15836 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 16.10 % Favored : 83.54 % Rotamer: Outliers : 0.50 % Allowed : 7.66 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 3.18 % Twisted General : 0.52 % 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: -5.70 (0.08), residues: 4965 helix: -4.04 (0.07), residues: 1472 sheet: -3.22 (0.22), residues: 427 loop : -3.96 (0.09), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 292 TYR 0.040 0.002 TYR O 132 PHE 0.037 0.003 PHE O 191 TRP 0.027 0.002 TRP B 442 HIS 0.016 0.002 HIS M 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.26 (41361) covalent geometry : angle 1.14087 / 0.61 (56036) hydrogen bonds : bond 0.25896 / 17.35 ( 908) hydrogen bonds : angle 9.12674 / 6.13 ( 2571) metal coordination : bond 0.39907 / 18.24 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 525 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.1499 (ttm-80) cc_final: 0.0515 (mtt90) REVERT: A 140 ILE cc_start: -0.2083 (OUTLIER) cc_final: -0.2413 (mp) REVERT: A 274 MET cc_start: 0.4391 (mmm) cc_final: 0.2409 (pmm) REVERT: A 688 GLN cc_start: 0.1259 (tp40) cc_final: 0.0299 (tp40) REVERT: A 703 ARG cc_start: 0.3631 (mpt90) cc_final: 0.2137 (mmt180) REVERT: A 1174 GLN cc_start: 0.4131 (tt0) cc_final: 0.3913 (pt0) REVERT: A 1343 MET cc_start: 0.1853 (ttt) cc_final: 0.0810 (mmt) REVERT: B 171 MET cc_start: -0.1964 (mmm) cc_final: -0.2314 (mtt) REVERT: C 47 LEU cc_start: 0.0348 (tt) cc_final: -0.0309 (mt) REVERT: D 107 MET cc_start: 0.2098 (ttt) cc_final: 0.0986 (tpt) REVERT: E 1 MET cc_start: -0.1031 (tpt) cc_final: -0.1759 (mtm) REVERT: E 72 PHE cc_start: -0.1928 (m-80) cc_final: -0.2548 (m-80) REVERT: N 297 MET cc_start: -0.2914 (tpp) cc_final: -0.3634 (ptp) REVERT: P 172 ILE cc_start: 0.5387 (tp) cc_final: 0.4897 (tp) outliers start: 22 outliers final: 9 residues processed: 543 average time/residue: 0.2602 time to fit residues: 230.8804 Evaluate side-chains 335 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 325 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain Q residue 59 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.0980 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 494 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 HIS A 328 ASN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 643 ASN A 805 ASN A 808 GLN A 828 GLN A 838 ASN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN A1318 HIS B 197 GLN B 217 GLN B 244 HIS B 286 ASN B 334 HIS B 552 ASN B 600 HIS ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN B 733 GLN B 754 ASN B 774 ASN B 821 HIS B 840 GLN B 883 GLN B 891 ASN B 902 GLN B 903 ASN ** B 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B1049 GLN B1130 GLN B1148 GLN C 10 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 71 ASN D 125 ASN E 5 ASN E 54 GLN E 99 HIS E 104 ASN E 114 ASN E 136 ASN E 146 HIS G 36 ASN G 69 ASN G 176 ASN H 83 GLN H 133 ASN H 134 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN M 155 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS N 366 HIS N 377 ASN O 43 ASN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 HIS O 225 ASN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 337 GLN O 456 HIS O 464 ASN ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 599 ASN O 631 ASN P 214 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.237733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.213594 restraints weight = 60620.029| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 1.78 r_work: 0.4100 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4101 r_free = 0.4101 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4101 r_free = 0.4101 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0500 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 41369 Z= 0.173 Angle : 0.812 13.628 56036 Z= 0.418 Chirality : 0.048 0.230 6312 Planarity : 0.006 0.076 7090 Dihedral : 11.754 84.459 5926 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.49 % Favored : 84.27 % Rotamer: Outliers : 2.35 % Allowed : 10.30 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 2.27 % Twisted General : 0.40 % 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: -4.87 (0.09), residues: 4965 helix: -2.79 (0.10), residues: 1510 sheet: -2.84 (0.23), residues: 431 loop : -3.74 (0.09), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 90 TYR 0.030 0.002 TYR O 132 PHE 0.024 0.002 PHE A1257 TRP 0.026 0.002 TRP O 648 HIS 0.010 0.002 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (41361) covalent geometry : angle 0.81243 / 0.42 (56036) hydrogen bonds : bond 0.05029 / 3.41 ( 908) hydrogen bonds : angle 5.96879 / 4.09 ( 2571) metal coordination : bond 0.02400 / 1.22 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 375 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.4500 (p) cc_final: 0.4253 (m) REVERT: A 117 GLU cc_start: 0.2817 (mm-30) cc_final: 0.2339 (tt0) REVERT: A 124 LEU cc_start: 0.0393 (mt) cc_final: 0.0072 (mp) REVERT: A 140 ILE cc_start: -0.2012 (OUTLIER) cc_final: -0.2521 (mp) REVERT: A 313 MET cc_start: 0.4799 (ppp) cc_final: 0.2812 (mmp) REVERT: A 697 MET cc_start: 0.1345 (tpt) cc_final: 0.0829 (tpp) REVERT: A 1291 ARG cc_start: 0.0581 (OUTLIER) cc_final: -0.0255 (ptp90) REVERT: A 1348 MET cc_start: 0.0995 (mmt) cc_final: -0.0223 (tpp) REVERT: A 1419 GLN cc_start: 0.3886 (tp-100) cc_final: 0.3047 (mm110) REVERT: B 171 MET cc_start: -0.1306 (mmm) cc_final: -0.1987 (mmm) REVERT: B 272 VAL cc_start: 0.1837 (m) cc_final: 0.1551 (p) REVERT: B 286 ASN cc_start: 0.2191 (OUTLIER) cc_final: 0.1084 (m-40) REVERT: B 292 LYS cc_start: 0.3997 (OUTLIER) cc_final: 0.2994 (tptt) REVERT: B 771 LEU cc_start: -0.4808 (OUTLIER) cc_final: -0.5018 (pp) REVERT: B 891 ASN cc_start: 0.4363 (OUTLIER) cc_final: 0.3464 (t0) REVERT: B 958 MET cc_start: 0.0449 (tpp) cc_final: -0.2066 (mmp) REVERT: B 1103 TYR cc_start: 0.1118 (p90) cc_final: -0.0384 (p90) REVERT: D 107 MET cc_start: 0.0525 (ttt) cc_final: -0.0288 (tpt) REVERT: D 131 MET cc_start: 0.2690 (mtp) cc_final: 0.1346 (tpt) REVERT: E 1 MET cc_start: -0.0256 (tpt) cc_final: -0.1423 (mtp) REVERT: E 50 MET cc_start: 0.0288 (pmm) cc_final: -0.0331 (ppp) REVERT: G 45 CYS cc_start: 0.1636 (p) cc_final: 0.1088 (m) REVERT: K 142 MET cc_start: 0.2131 (mtm) cc_final: 0.0936 (mmt) REVERT: N 297 MET cc_start: -0.3392 (tpp) cc_final: -0.3932 (ptp) REVERT: N 305 MET cc_start: -0.0714 (mtm) cc_final: -0.1072 (ttp) REVERT: O 35 SER cc_start: 0.4657 (OUTLIER) cc_final: 0.4225 (t) REVERT: O 271 LEU cc_start: 0.1922 (OUTLIER) cc_final: 0.1425 (mp) REVERT: P 166 THR cc_start: 0.2322 (p) cc_final: 0.2080 (m) outliers start: 103 outliers final: 39 residues processed: 459 average time/residue: 0.2448 time to fit residues: 188.8185 Evaluate side-chains 341 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 891 ASN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain N residue 366 HIS Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 78 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 204 optimal weight: 0.8980 chunk 388 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 417 optimal weight: 0.7980 chunk 317 optimal weight: 0.6980 chunk 171 optimal weight: 9.9990 chunk 255 optimal weight: 0.0980 chunk 202 optimal weight: 0.0980 chunk 346 optimal weight: 0.0270 chunk 271 optimal weight: 0.7980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A 805 ASN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS B 286 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 ASN ** B 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1077 GLN C 65 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN E 99 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 GLN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 258 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.242324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.220045 restraints weight = 67585.972| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 1.91 r_work: 0.4193 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4200 r_free = 0.4200 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4200 r_free = 0.4200 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0517 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41369 Z= 0.133 Angle : 0.739 12.227 56036 Z= 0.377 Chirality : 0.046 0.229 6312 Planarity : 0.005 0.086 7090 Dihedral : 11.528 85.281 5920 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.99 % Favored : 84.79 % Rotamer: Outliers : 2.32 % Allowed : 12.21 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 2.73 % Twisted General : 0.31 % 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: -4.31 (0.10), residues: 4965 helix: -2.04 (0.12), residues: 1491 sheet: -2.57 (0.24), residues: 416 loop : -3.55 (0.10), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 149 TYR 0.025 0.001 TYR O 132 PHE 0.026 0.001 PHE M 74 TRP 0.017 0.001 TRP O 583 HIS 0.009 0.001 HIS O 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (41361) covalent geometry : angle 0.73921 / 0.38 (56036) hydrogen bonds : bond 0.04063 / 2.74 ( 908) hydrogen bonds : angle 5.33219 / 3.64 ( 2571) metal coordination : bond 0.00456 / 0.17 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 315 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.2532 (mm-30) cc_final: 0.2314 (tt0) REVERT: A 124 LEU cc_start: 0.0322 (mt) cc_final: -0.0030 (mp) REVERT: A 274 MET cc_start: 0.3353 (mmt) cc_final: 0.3009 (mmt) REVERT: A 313 MET cc_start: 0.4563 (ppp) cc_final: 0.3026 (mmp) REVERT: A 1174 GLN cc_start: 0.4301 (tm-30) cc_final: 0.3905 (pp30) REVERT: A 1348 MET cc_start: 0.0554 (mmt) cc_final: -0.0762 (tpp) REVERT: B 171 MET cc_start: -0.1252 (mmm) cc_final: -0.1969 (mmm) REVERT: B 286 ASN cc_start: 0.2702 (OUTLIER) cc_final: 0.0870 (t0) REVERT: B 695 GLN cc_start: -0.1558 (OUTLIER) cc_final: -0.2478 (pt0) REVERT: B 728 MET cc_start: 0.3591 (mmm) cc_final: 0.3221 (mmm) REVERT: B 735 MET cc_start: 0.0803 (ptm) cc_final: -0.0532 (mmt) REVERT: B 945 ASN cc_start: 0.1261 (p0) cc_final: 0.0935 (p0) REVERT: B 1103 TYR cc_start: 0.1191 (p90) cc_final: -0.0434 (p90) REVERT: D 131 MET cc_start: 0.3797 (mtp) cc_final: 0.2376 (tpt) REVERT: E 1 MET cc_start: 0.0072 (tpt) cc_final: -0.1044 (mtt) REVERT: F 85 MET cc_start: 0.0173 (tmm) cc_final: -0.0180 (mmm) REVERT: G 168 LEU cc_start: 0.0803 (mt) cc_final: 0.0525 (mt) REVERT: K 142 MET cc_start: 0.1733 (mtm) cc_final: 0.0757 (mmt) REVERT: N 297 MET cc_start: -0.2988 (tpp) cc_final: -0.3702 (ptp) REVERT: N 305 MET cc_start: -0.0195 (OUTLIER) cc_final: -0.0395 (ttm) REVERT: O 35 SER cc_start: 0.4371 (OUTLIER) cc_final: 0.4011 (t) REVERT: O 139 GLU cc_start: 0.5667 (mm-30) cc_final: 0.4731 (tt0) REVERT: O 271 LEU cc_start: 0.2092 (OUTLIER) cc_final: 0.1620 (mp) REVERT: O 326 ILE cc_start: 0.1877 (OUTLIER) cc_final: 0.0255 (tp) REVERT: O 577 MET cc_start: 0.2575 (tpp) cc_final: 0.1760 (tpp) REVERT: P 166 THR cc_start: 0.2679 (p) cc_final: 0.2412 (m) REVERT: P 172 ILE cc_start: 0.5706 (tp) cc_final: 0.4987 (tp) outliers start: 102 outliers final: 47 residues processed: 395 average time/residue: 0.2379 time to fit residues: 159.9584 Evaluate side-chains 339 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 286 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 397 optimal weight: 4.9990 chunk 24 optimal weight: 0.0170 chunk 36 optimal weight: 0.7980 chunk 156 optimal weight: 0.4980 chunk 449 optimal weight: 7.9990 chunk 478 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 256 optimal weight: 3.9990 chunk 374 optimal weight: 0.0020 chunk 362 optimal weight: 0.9980 chunk 381 optimal weight: 4.9990 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 HIS B 286 ASN B 574 GLN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 136 ASN H 3 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.243532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.222622 restraints weight = 61380.532| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 1.52 r_work: 0.4254 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4259 r_free = 0.4259 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4259 r_free = 0.4259 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0611 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 41369 Z= 0.128 Angle : 0.714 12.489 56036 Z= 0.364 Chirality : 0.045 0.227 6312 Planarity : 0.005 0.083 7090 Dihedral : 11.387 85.232 5918 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 15.47 % Favored : 84.33 % Rotamer: Outliers : 2.14 % Allowed : 13.81 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 2.27 % Twisted General : 0.29 % 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: -4.02 (0.11), residues: 4965 helix: -1.63 (0.13), residues: 1476 sheet: -2.40 (0.24), residues: 412 loop : -3.46 (0.10), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 696 TYR 0.023 0.001 TYR O 494 PHE 0.028 0.001 PHE G 105 TRP 0.015 0.001 TRP O 583 HIS 0.009 0.001 HIS O 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (41361) covalent geometry : angle 0.71425 / 0.36 (56036) hydrogen bonds : bond 0.03526 / 2.40 ( 908) hydrogen bonds : angle 5.06630 / 3.46 ( 2571) metal coordination : bond 0.00207 / 0.09 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 313 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.4570 (ppp) cc_final: 0.3091 (mmp) REVERT: A 540 ASN cc_start: -0.0167 (m-40) cc_final: -0.0584 (m-40) REVERT: A 1161 VAL cc_start: 0.0752 (p) cc_final: 0.0190 (t) REVERT: A 1348 MET cc_start: 0.0479 (mmt) cc_final: -0.0803 (tpp) REVERT: B 171 MET cc_start: -0.0921 (mmm) cc_final: -0.1746 (mmm) REVERT: B 286 ASN cc_start: 0.3214 (OUTLIER) cc_final: 0.1531 (m-40) REVERT: B 695 GLN cc_start: -0.1371 (OUTLIER) cc_final: -0.2278 (pt0) REVERT: B 728 MET cc_start: 0.3866 (mmm) cc_final: 0.3614 (mmm) REVERT: B 735 MET cc_start: 0.0562 (ptm) cc_final: -0.0509 (mmt) REVERT: B 885 MET cc_start: 0.2953 (pmm) cc_final: 0.2179 (pmm) REVERT: B 1103 TYR cc_start: 0.1382 (p90) cc_final: -0.0535 (p90) REVERT: B 1133 LEU cc_start: 0.1530 (OUTLIER) cc_final: 0.1279 (mp) REVERT: D 131 MET cc_start: 0.3870 (mtp) cc_final: 0.2525 (tpt) REVERT: E 1 MET cc_start: 0.0279 (tpt) cc_final: -0.0832 (mtt) REVERT: F 85 MET cc_start: 0.0126 (tmm) cc_final: -0.0187 (mmm) REVERT: K 142 MET cc_start: 0.1646 (mtm) cc_final: 0.0720 (mmt) REVERT: M 179 LEU cc_start: 0.0587 (OUTLIER) cc_final: -0.0180 (mt) REVERT: N 305 MET cc_start: -0.0062 (mtm) cc_final: -0.0263 (ttm) REVERT: O 35 SER cc_start: 0.4210 (OUTLIER) cc_final: 0.3924 (t) REVERT: O 139 GLU cc_start: 0.5336 (mm-30) cc_final: 0.4564 (tt0) REVERT: O 190 LEU cc_start: 0.3365 (OUTLIER) cc_final: 0.3096 (tt) REVERT: O 236 LYS cc_start: 0.1289 (tptt) cc_final: 0.0974 (tptp) REVERT: O 271 LEU cc_start: 0.2058 (OUTLIER) cc_final: 0.1610 (mp) REVERT: O 326 ILE cc_start: 0.1718 (OUTLIER) cc_final: 0.1004 (tp) REVERT: P 166 THR cc_start: 0.2848 (p) cc_final: 0.2515 (m) outliers start: 94 outliers final: 61 residues processed: 380 average time/residue: 0.2405 time to fit residues: 155.0595 Evaluate side-chains 350 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 281 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 937 ARG Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 140 TRP Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 310 VAL Chi-restraints excluded: chain Q residue 78 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 191 optimal weight: 1.9990 chunk 476 optimal weight: 0.4980 chunk 403 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 187 optimal weight: 0.9980 chunk 459 optimal weight: 5.9990 chunk 416 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 138 optimal weight: 0.0010 chunk 150 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 HIS B 286 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 136 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 GLN ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 337 GLN O 456 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.245347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.223677 restraints weight = 64551.352| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 1.65 r_work: 0.4244 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4248 r_free = 0.4248 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4248 r_free = 0.4248 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0742 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41369 Z= 0.122 Angle : 0.694 13.346 56036 Z= 0.352 Chirality : 0.044 0.227 6312 Planarity : 0.005 0.082 7090 Dihedral : 11.248 84.473 5916 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 15.19 % Favored : 84.61 % Rotamer: Outliers : 2.89 % Allowed : 14.24 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.27 % 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: -3.81 (0.11), residues: 4965 helix: -1.37 (0.13), residues: 1492 sheet: -2.34 (0.24), residues: 410 loop : -3.37 (0.10), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 643 TYR 0.030 0.001 TYR B 164 PHE 0.023 0.001 PHE O 249 TRP 0.016 0.001 TRP O 583 HIS 0.011 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (41361) covalent geometry : angle 0.69436 / 0.35 (56036) hydrogen bonds : bond 0.03332 / 2.26 ( 908) hydrogen bonds : angle 4.88413 / 3.33 ( 2571) metal coordination : bond 0.00240 / 0.12 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 298 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: -0.2111 (OUTLIER) cc_final: -0.2669 (mp) REVERT: A 313 MET cc_start: 0.4559 (ppp) cc_final: 0.3105 (mmp) REVERT: A 849 ARG cc_start: 0.1452 (OUTLIER) cc_final: 0.0493 (tpm170) REVERT: A 1161 VAL cc_start: 0.0507 (p) cc_final: -0.0020 (t) REVERT: A 1174 GLN cc_start: 0.4343 (tm-30) cc_final: 0.4040 (tm-30) REVERT: A 1348 MET cc_start: 0.0500 (mmt) cc_final: -0.0921 (tpp) REVERT: B 272 VAL cc_start: 0.1895 (m) cc_final: 0.1612 (p) REVERT: B 286 ASN cc_start: 0.2950 (OUTLIER) cc_final: 0.0954 (m-40) REVERT: B 590 ILE cc_start: -0.1605 (OUTLIER) cc_final: -0.1826 (mp) REVERT: B 695 GLN cc_start: -0.1000 (OUTLIER) cc_final: -0.1911 (pt0) REVERT: B 735 MET cc_start: 0.0582 (ptm) cc_final: -0.0381 (mmt) REVERT: B 844 ASN cc_start: 0.3718 (t0) cc_final: 0.1983 (t0) REVERT: B 1133 LEU cc_start: 0.1308 (OUTLIER) cc_final: 0.1054 (mp) REVERT: D 58 ILE cc_start: 0.3314 (OUTLIER) cc_final: 0.2487 (mp) REVERT: D 131 MET cc_start: 0.3603 (mtp) cc_final: 0.2161 (tpt) REVERT: D 153 MET cc_start: 0.0111 (mmm) cc_final: -0.0253 (mmm) REVERT: E 1 MET cc_start: 0.0283 (tpt) cc_final: -0.0666 (mtp) REVERT: F 85 MET cc_start: 0.0075 (mmm) cc_final: -0.0382 (mmm) REVERT: F 99 LEU cc_start: 0.2027 (OUTLIER) cc_final: 0.1466 (pp) REVERT: K 142 MET cc_start: 0.1691 (mtm) cc_final: 0.0763 (mmt) REVERT: M 118 LEU cc_start: 0.0221 (OUTLIER) cc_final: -0.0339 (mt) REVERT: M 179 LEU cc_start: 0.0728 (OUTLIER) cc_final: -0.0224 (mt) REVERT: N 305 MET cc_start: 0.0031 (mtm) cc_final: -0.0306 (ttm) REVERT: O 35 SER cc_start: 0.4289 (OUTLIER) cc_final: 0.3962 (t) REVERT: O 121 TYR cc_start: 0.5142 (m-80) cc_final: 0.3692 (m-80) REVERT: O 139 GLU cc_start: 0.5194 (mm-30) cc_final: 0.4477 (tt0) REVERT: O 140 ILE cc_start: 0.4758 (mt) cc_final: 0.4396 (mt) REVERT: O 190 LEU cc_start: 0.3402 (OUTLIER) cc_final: 0.3104 (tt) REVERT: O 236 LYS cc_start: 0.1118 (tptt) cc_final: 0.0827 (tptp) REVERT: O 271 LEU cc_start: 0.2064 (OUTLIER) cc_final: 0.1719 (mp) REVERT: O 326 ILE cc_start: 0.1710 (OUTLIER) cc_final: 0.0450 (tp) REVERT: O 528 MET cc_start: 0.3553 (mmm) cc_final: 0.3296 (mpp) REVERT: P 166 THR cc_start: 0.2828 (p) cc_final: 0.2512 (m) REVERT: P 299 MET cc_start: 0.3892 (pmm) cc_final: 0.3536 (ptt) outliers start: 127 outliers final: 69 residues processed: 397 average time/residue: 0.2330 time to fit residues: 158.2972 Evaluate side-chains 361 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 278 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 140 TRP Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 132 TYR Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 310 VAL Chi-restraints excluded: chain Q residue 78 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 456 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 200 optimal weight: 0.0270 chunk 403 optimal weight: 0.7980 chunk 383 optimal weight: 0.4980 chunk 419 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 490 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 142 optimal weight: 0.0370 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 HIS B 286 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.246591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.227023 restraints weight = 72370.366| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 1.89 r_work: 0.4262 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4272 r_free = 0.4272 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4272 r_free = 0.4272 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0816 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 41369 Z= 0.119 Angle : 0.685 14.369 56036 Z= 0.347 Chirality : 0.044 0.227 6312 Planarity : 0.005 0.079 7090 Dihedral : 11.134 84.580 5916 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.17 % Favored : 84.61 % Rotamer: Outliers : 2.69 % Allowed : 14.47 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.25 % 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: -3.68 (0.11), residues: 4965 helix: -1.17 (0.13), residues: 1505 sheet: -2.38 (0.24), residues: 432 loop : -3.33 (0.10), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 303 TYR 0.018 0.001 TYR O 494 PHE 0.023 0.001 PHE M 162 TRP 0.016 0.001 TRP O 583 HIS 0.008 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (41361) covalent geometry : angle 0.68547 / 0.35 (56036) hydrogen bonds : bond 0.03213 / 2.20 ( 908) hydrogen bonds : angle 4.74938 / 3.23 ( 2571) metal coordination : bond 0.00184 / 0.09 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 290 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: -0.2169 (OUTLIER) cc_final: -0.2756 (mp) REVERT: A 313 MET cc_start: 0.4657 (ppp) cc_final: 0.3191 (mmp) REVERT: A 326 TYR cc_start: 0.3468 (t80) cc_final: 0.2065 (t80) REVERT: A 583 MET cc_start: 0.1705 (tmm) cc_final: 0.1284 (tmm) REVERT: A 735 TYR cc_start: 0.0888 (m-10) cc_final: 0.0428 (m-80) REVERT: A 849 ARG cc_start: 0.1445 (OUTLIER) cc_final: 0.0443 (tpp-160) REVERT: A 1161 VAL cc_start: 0.0482 (p) cc_final: -0.0009 (t) REVERT: A 1260 MET cc_start: 0.0037 (OUTLIER) cc_final: -0.0344 (mtt) REVERT: A 1348 MET cc_start: 0.0543 (mmt) cc_final: -0.0748 (tpp) REVERT: B 286 ASN cc_start: 0.3489 (OUTLIER) cc_final: 0.2773 (t0) REVERT: B 695 GLN cc_start: -0.0919 (OUTLIER) cc_final: -0.1870 (pt0) REVERT: B 735 MET cc_start: 0.0544 (ptm) cc_final: -0.0302 (mmt) REVERT: B 944 MET cc_start: -0.2399 (mmm) cc_final: -0.2851 (ptp) REVERT: B 1133 LEU cc_start: 0.1317 (OUTLIER) cc_final: 0.1032 (mp) REVERT: D 58 ILE cc_start: 0.3446 (OUTLIER) cc_final: 0.2707 (mp) REVERT: D 131 MET cc_start: 0.3525 (mtp) cc_final: 0.2199 (tpt) REVERT: D 153 MET cc_start: 0.0274 (mmm) cc_final: -0.0126 (mmm) REVERT: E 1 MET cc_start: 0.0251 (tpt) cc_final: -0.0791 (mtt) REVERT: F 85 MET cc_start: 0.0129 (mmm) cc_final: -0.0409 (mmm) REVERT: K 142 MET cc_start: 0.1709 (mtm) cc_final: 0.0792 (mmt) REVERT: M 118 LEU cc_start: 0.0166 (OUTLIER) cc_final: -0.0443 (mt) REVERT: M 179 LEU cc_start: 0.0743 (OUTLIER) cc_final: -0.0134 (mt) REVERT: N 297 MET cc_start: -0.2140 (mmt) cc_final: -0.3680 (ttm) REVERT: N 305 MET cc_start: -0.0142 (OUTLIER) cc_final: -0.0360 (ttm) REVERT: O 35 SER cc_start: 0.4424 (OUTLIER) cc_final: 0.4074 (t) REVERT: O 69 VAL cc_start: -0.2116 (OUTLIER) cc_final: -0.3367 (t) REVERT: O 121 TYR cc_start: 0.5172 (m-80) cc_final: 0.3663 (m-80) REVERT: O 139 GLU cc_start: 0.5161 (mm-30) cc_final: 0.4707 (tt0) REVERT: O 140 ILE cc_start: 0.4854 (mt) cc_final: 0.4428 (mt) REVERT: O 190 LEU cc_start: 0.3378 (OUTLIER) cc_final: 0.3115 (tt) REVERT: O 271 LEU cc_start: 0.2101 (OUTLIER) cc_final: 0.1810 (mp) REVERT: O 326 ILE cc_start: 0.1683 (OUTLIER) cc_final: 0.0428 (tp) REVERT: O 598 GLU cc_start: 0.2328 (mt-10) cc_final: 0.0882 (tt0) REVERT: P 166 THR cc_start: 0.2992 (p) cc_final: 0.2692 (m) REVERT: P 299 MET cc_start: 0.3741 (pmm) cc_final: 0.3463 (ptt) outliers start: 118 outliers final: 77 residues processed: 380 average time/residue: 0.2144 time to fit residues: 142.6514 Evaluate side-chains 365 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 273 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 140 TRP Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 132 TYR Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 452 LEU Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 484 MET Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 310 VAL Chi-restraints excluded: chain Q residue 78 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 412 optimal weight: 5.9990 chunk 325 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 386 optimal weight: 0.0060 chunk 176 optimal weight: 0.5980 chunk 466 optimal weight: 10.0000 chunk 270 optimal weight: 0.0270 chunk 482 optimal weight: 20.0000 chunk 479 optimal weight: 0.0670 chunk 266 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN A 477 GLN B 61 HIS B 286 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 HIS ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 456 HIS ** 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 = 0.4684 r_free = 0.4684 target = 0.248253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.228220 restraints weight = 71219.783| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 1.65 r_work: 0.4297 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0975 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 41369 Z= 0.123 Angle : 0.686 14.582 56036 Z= 0.348 Chirality : 0.044 0.288 6312 Planarity : 0.005 0.082 7090 Dihedral : 11.057 83.487 5916 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.81 % Favored : 84.99 % Rotamer: Outliers : 2.67 % Allowed : 14.76 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.25 % 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: -3.55 (0.11), residues: 4965 helix: -0.98 (0.13), residues: 1491 sheet: -2.33 (0.24), residues: 421 loop : -3.28 (0.10), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 561 TYR 0.017 0.001 TYR O 494 PHE 0.023 0.001 PHE O 249 TRP 0.017 0.001 TRP O 583 HIS 0.017 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (41361) covalent geometry : angle 0.68573 / 0.35 (56036) hydrogen bonds : bond 0.03040 / 2.09 ( 908) hydrogen bonds : angle 4.70052 / 3.19 ( 2571) metal coordination : bond 0.00243 / 0.13 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 292 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: -0.1997 (OUTLIER) cc_final: -0.2585 (mp) REVERT: A 313 MET cc_start: 0.4757 (ppp) cc_final: 0.3273 (mmp) REVERT: A 735 TYR cc_start: 0.0900 (m-10) cc_final: -0.0936 (m-10) REVERT: A 794 MET cc_start: -0.2576 (tpp) cc_final: -0.3022 (mtt) REVERT: A 849 ARG cc_start: 0.1529 (OUTLIER) cc_final: 0.0720 (ptp90) REVERT: A 1348 MET cc_start: 0.0385 (mmt) cc_final: -0.0761 (tpp) REVERT: B 61 HIS cc_start: 0.2080 (OUTLIER) cc_final: 0.1743 (m90) REVERT: B 272 VAL cc_start: 0.2174 (m) cc_final: 0.1815 (p) REVERT: B 286 ASN cc_start: 0.3818 (OUTLIER) cc_final: 0.2632 (m110) REVERT: B 695 GLN cc_start: -0.0573 (OUTLIER) cc_final: -0.1541 (pt0) REVERT: B 728 MET cc_start: 0.4423 (mmm) cc_final: 0.3633 (mmm) REVERT: B 735 MET cc_start: 0.0406 (ptm) cc_final: -0.0324 (mmt) REVERT: B 844 ASN cc_start: 0.3815 (t0) cc_final: 0.1882 (t0) REVERT: B 944 MET cc_start: -0.1753 (mmm) cc_final: -0.2655 (ptp) REVERT: B 1133 LEU cc_start: 0.1706 (OUTLIER) cc_final: 0.1414 (mp) REVERT: D 131 MET cc_start: 0.3683 (mtp) cc_final: 0.2466 (tpt) REVERT: D 153 MET cc_start: 0.0741 (mmm) cc_final: 0.0464 (mmm) REVERT: E 1 MET cc_start: 0.0228 (tpt) cc_final: -0.0720 (mtt) REVERT: F 85 MET cc_start: 0.0155 (mmm) cc_final: -0.0486 (mmm) REVERT: K 142 MET cc_start: 0.1630 (mtm) cc_final: 0.0715 (mmt) REVERT: M 179 LEU cc_start: 0.0701 (OUTLIER) cc_final: -0.0170 (mt) REVERT: N 297 MET cc_start: -0.2430 (mmt) cc_final: -0.4077 (mtt) REVERT: N 305 MET cc_start: -0.0154 (mtm) cc_final: -0.0416 (ttm) REVERT: O 35 SER cc_start: 0.4542 (OUTLIER) cc_final: 0.4168 (t) REVERT: O 69 VAL cc_start: -0.2081 (OUTLIER) cc_final: -0.3315 (t) REVERT: O 140 ILE cc_start: 0.5115 (mt) cc_final: 0.4852 (mt) REVERT: O 190 LEU cc_start: 0.3454 (OUTLIER) cc_final: 0.3186 (tt) REVERT: O 326 ILE cc_start: 0.1786 (OUTLIER) cc_final: 0.0482 (tp) REVERT: P 299 MET cc_start: 0.3686 (pmm) cc_final: 0.3472 (ptt) outliers start: 117 outliers final: 79 residues processed: 378 average time/residue: 0.2268 time to fit residues: 148.0771 Evaluate side-chains 359 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 269 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 140 TRP Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 132 TYR Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 452 LEU Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 484 MET Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 310 VAL Chi-restraints excluded: chain Q residue 78 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 371 optimal weight: 0.0670 chunk 393 optimal weight: 0.5980 chunk 310 optimal weight: 0.2980 chunk 153 optimal weight: 9.9990 chunk 262 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 361 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 70 optimal weight: 0.0970 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 ASN A 949 ASN B 61 HIS B 298 GLN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 366 HIS ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 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 = 0.4692 r_free = 0.4692 target = 0.249251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.230259 restraints weight = 63557.352| |-----------------------------------------------------------------------------| r_work (start): 0.4515 rms_B_bonded: 1.46 r_work: 0.4324 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4329 r_free = 0.4329 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4329 r_free = 0.4329 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1042 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 41369 Z= 0.116 Angle : 0.684 16.712 56036 Z= 0.343 Chirality : 0.044 0.261 6312 Planarity : 0.005 0.079 7090 Dihedral : 11.007 83.617 5916 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.79 % Favored : 85.03 % Rotamer: Outliers : 2.48 % Allowed : 15.06 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.25 % 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: -3.43 (0.11), residues: 4965 helix: -0.87 (0.13), residues: 1499 sheet: -2.19 (0.25), residues: 384 loop : -3.23 (0.10), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 136 TYR 0.015 0.001 TYR O 494 PHE 0.013 0.001 PHE B 587 TRP 0.016 0.001 TRP G 128 HIS 0.008 0.001 HIS O 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (41361) covalent geometry : angle 0.68445 / 0.34 (56036) hydrogen bonds : bond 0.02906 / 2.00 ( 908) hydrogen bonds : angle 4.62364 / 3.14 ( 2571) metal coordination : bond 0.00181 / 0.09 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 285 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: -0.1893 (OUTLIER) cc_final: -0.2504 (mp) REVERT: A 261 LEU cc_start: 0.1693 (tp) cc_final: 0.1303 (tt) REVERT: A 313 MET cc_start: 0.4883 (ppp) cc_final: 0.3250 (mmp) REVERT: A 582 MET cc_start: -0.0090 (tpp) cc_final: -0.0705 (ttm) REVERT: A 735 TYR cc_start: 0.1161 (m-10) cc_final: -0.1564 (m-10) REVERT: A 794 MET cc_start: -0.2390 (tpp) cc_final: -0.3048 (mtt) REVERT: A 849 ARG cc_start: 0.1560 (OUTLIER) cc_final: 0.0621 (tpm170) REVERT: A 1348 MET cc_start: 0.0493 (mmt) cc_final: -0.0596 (tpp) REVERT: B 272 VAL cc_start: 0.2078 (m) cc_final: 0.1740 (p) REVERT: B 517 MET cc_start: 0.1191 (mmp) cc_final: -0.0101 (ptt) REVERT: B 695 GLN cc_start: -0.0306 (OUTLIER) cc_final: -0.1322 (pt0) REVERT: B 728 MET cc_start: 0.4852 (mmm) cc_final: 0.4019 (mmm) REVERT: B 735 MET cc_start: 0.0585 (ptm) cc_final: -0.0082 (mmt) REVERT: B 844 ASN cc_start: 0.3889 (t0) cc_final: 0.2115 (t0) REVERT: B 944 MET cc_start: -0.1694 (mmm) cc_final: -0.3118 (ptp) REVERT: D 131 MET cc_start: 0.3551 (mtp) cc_final: 0.2419 (tpt) REVERT: D 153 MET cc_start: 0.0874 (mmm) cc_final: 0.0548 (mmm) REVERT: E 1 MET cc_start: 0.0166 (tpt) cc_final: -0.0570 (mtp) REVERT: E 93 MET cc_start: 0.1633 (ppp) cc_final: 0.1114 (ppp) REVERT: F 85 MET cc_start: 0.0201 (mmm) cc_final: -0.0469 (mmm) REVERT: K 142 MET cc_start: 0.1630 (mtm) cc_final: 0.0716 (mmt) REVERT: M 179 LEU cc_start: 0.0622 (OUTLIER) cc_final: -0.0149 (mt) REVERT: N 297 MET cc_start: -0.2451 (mmt) cc_final: -0.4044 (mtt) REVERT: N 305 MET cc_start: -0.0121 (mtm) cc_final: -0.0337 (ttm) REVERT: N 366 HIS cc_start: 0.0463 (OUTLIER) cc_final: -0.0026 (m170) REVERT: O 69 VAL cc_start: -0.2080 (OUTLIER) cc_final: -0.3290 (t) REVERT: O 140 ILE cc_start: 0.5452 (mt) cc_final: 0.5083 (mt) REVERT: O 326 ILE cc_start: 0.1861 (OUTLIER) cc_final: 0.0441 (tp) REVERT: O 598 GLU cc_start: 0.2190 (mt-10) cc_final: 0.1114 (tt0) outliers start: 109 outliers final: 90 residues processed: 370 average time/residue: 0.2348 time to fit residues: 149.5262 Evaluate side-chains 365 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 268 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 140 TRP Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 366 HIS Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 132 TYR Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 452 LEU Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 484 MET Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain O residue 581 LEU Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 310 VAL Chi-restraints excluded: chain Q residue 78 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 35 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 375 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 350 optimal weight: 0.9980 chunk 309 optimal weight: 0.6980 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 4.9990 chunk 457 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 558 ASN ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN C 99 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 366 HIS ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 456 HIS ** 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 = 0.4728 r_free = 0.4728 target = 0.253488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.233938 restraints weight = 73626.769| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 1.60 r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4549 r_free = 0.4549 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4549 r_free = 0.4549 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1605 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 41369 Z= 0.173 Angle : 0.780 20.458 56036 Z= 0.400 Chirality : 0.047 0.485 6312 Planarity : 0.006 0.084 7090 Dihedral : 11.076 78.827 5916 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.93 % Favored : 83.90 % Rotamer: Outliers : 2.55 % Allowed : 15.36 % Favored : 82.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.23 % 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: -3.57 (0.11), residues: 4965 helix: -0.98 (0.13), residues: 1499 sheet: -2.40 (0.24), residues: 397 loop : -3.29 (0.10), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 364 TYR 0.047 0.002 TYR B 241 PHE 0.023 0.002 PHE O 249 TRP 0.027 0.002 TRP J 18 HIS 0.077 0.003 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (41361) covalent geometry : angle 0.77974 / 0.40 (56036) hydrogen bonds : bond 0.04086 / 2.82 ( 908) hydrogen bonds : angle 4.93584 / 3.39 ( 2571) metal coordination : bond 0.00398 / 0.24 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 313 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.2016 (OUTLIER) cc_final: -0.1214 (tp30) REVERT: A 54 LEU cc_start: 0.2208 (OUTLIER) cc_final: 0.1829 (pp) REVERT: A 140 ILE cc_start: -0.1879 (OUTLIER) cc_final: -0.2371 (mp) REVERT: A 313 MET cc_start: 0.5443 (ppp) cc_final: 0.3427 (mmp) REVERT: A 583 MET cc_start: 0.1323 (OUTLIER) cc_final: 0.0218 (tmm) REVERT: A 694 MET cc_start: 0.1508 (mmm) cc_final: 0.0683 (mmm) REVERT: A 735 TYR cc_start: 0.1574 (m-10) cc_final: 0.0428 (m-10) REVERT: A 849 ARG cc_start: 0.2009 (OUTLIER) cc_final: 0.1219 (tpp-160) REVERT: A 1348 MET cc_start: 0.0845 (mmt) cc_final: -0.0530 (tpp) REVERT: B 133 ILE cc_start: -0.1276 (OUTLIER) cc_final: -0.1649 (pp) REVERT: B 695 GLN cc_start: 0.0981 (OUTLIER) cc_final: -0.0120 (pt0) REVERT: B 735 MET cc_start: 0.1219 (ptm) cc_final: 0.0416 (mmt) REVERT: B 842 TYR cc_start: 0.4451 (p90) cc_final: 0.4248 (p90) REVERT: B 885 MET cc_start: 0.3544 (pmm) cc_final: 0.2700 (ppp) REVERT: B 1091 GLU cc_start: 0.2800 (pm20) cc_final: 0.1832 (tt0) REVERT: C 1 MET cc_start: -0.2798 (OUTLIER) cc_final: -0.4027 (ttm) REVERT: D 131 MET cc_start: 0.3586 (mtp) cc_final: 0.3021 (tpt) REVERT: E 1 MET cc_start: 0.0273 (tpt) cc_final: -0.0399 (mtp) REVERT: E 93 MET cc_start: 0.1718 (ppp) cc_final: 0.1064 (ppp) REVERT: F 85 MET cc_start: 0.1009 (mmm) cc_final: -0.0271 (mmm) REVERT: F 151 LEU cc_start: 0.0571 (OUTLIER) cc_final: -0.2057 (mt) REVERT: J 2 ILE cc_start: 0.1954 (mp) cc_final: 0.0803 (mt) REVERT: K 142 MET cc_start: 0.2236 (mtm) cc_final: 0.1056 (mmt) REVERT: M 179 LEU cc_start: 0.0583 (OUTLIER) cc_final: -0.0224 (mt) REVERT: N 297 MET cc_start: -0.1417 (mmt) cc_final: -0.3222 (mtt) REVERT: N 305 MET cc_start: 0.0165 (mtm) cc_final: -0.0253 (ttm) REVERT: O 35 SER cc_start: 0.4459 (OUTLIER) cc_final: 0.4250 (t) REVERT: O 69 VAL cc_start: -0.1685 (OUTLIER) cc_final: -0.2703 (t) REVERT: O 326 ILE cc_start: 0.1407 (OUTLIER) cc_final: 0.0117 (tp) REVERT: P 172 ILE cc_start: 0.5306 (tp) cc_final: 0.4564 (tp) outliers start: 112 outliers final: 71 residues processed: 398 average time/residue: 0.2458 time to fit residues: 166.1699 Evaluate side-chains 359 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 275 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 132 TYR Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 452 LEU Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 484 MET Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 310 VAL Chi-restraints excluded: chain Q residue 78 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 182 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 462 optimal weight: 7.9990 chunk 324 optimal weight: 0.9980 chunk 478 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 343 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 466 optimal weight: 8.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN A 815 GLN A 936 ASN B 286 ASN B 425 HIS B 476 GLN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 207 HIS ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN O 616 ASN ** O 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.261335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.246290 restraints weight = 67045.249| |-----------------------------------------------------------------------------| r_work (start): 0.4653 rms_B_bonded: 1.20 r_work: 0.4457 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4465 r_free = 0.4465 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4465 r_free = 0.4465 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2621 moved from start: 0.7169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 41369 Z= 0.247 Angle : 0.976 26.877 56036 Z= 0.496 Chirality : 0.053 0.363 6312 Planarity : 0.008 0.163 7090 Dihedral : 11.392 81.319 5916 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.08 % Favored : 83.76 % Rotamer: Outliers : 2.21 % Allowed : 15.86 % Favored : 81.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.25 % 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: -3.93 (0.11), residues: 4965 helix: -1.45 (0.12), residues: 1511 sheet: -2.59 (0.25), residues: 351 loop : -3.44 (0.10), residues: 3103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.002 ARG O 578 TYR 0.065 0.003 TYR F 137 PHE 0.093 0.003 PHE F 143 TRP 0.034 0.003 TRP F 146 HIS 0.038 0.003 HIS N 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.25 (41361) covalent geometry : angle 0.97605 / 0.50 (56036) hydrogen bonds : bond 0.04717 / 3.30 ( 908) hydrogen bonds : angle 5.60679 / 3.88 ( 2571) metal coordination : bond 0.00480 / 0.26 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9930 Ramachandran restraints generated. 4965 Oldfield, 0 Emsley, 4965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 406 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.1968 (OUTLIER) cc_final: 0.0698 (pp20) REVERT: A 140 ILE cc_start: -0.0966 (OUTLIER) cc_final: -0.1407 (mp) REVERT: A 288 LYS cc_start: 0.5438 (tppt) cc_final: 0.5033 (tttp) REVERT: A 313 MET cc_start: 0.5201 (ppp) cc_final: 0.3929 (mmp) REVERT: A 694 MET cc_start: 0.1990 (mmm) cc_final: 0.1233 (mmm) REVERT: A 849 ARG cc_start: 0.2352 (OUTLIER) cc_final: 0.1495 (tpp-160) REVERT: A 1348 MET cc_start: 0.0797 (mmt) cc_final: -0.1296 (tpp) REVERT: A 1369 LEU cc_start: 0.2207 (OUTLIER) cc_final: 0.1708 (tt) REVERT: A 1379 MET cc_start: 0.0869 (tpt) cc_final: 0.0388 (ptm) REVERT: B 312 MET cc_start: 0.1833 (ppp) cc_final: 0.1166 (ppp) REVERT: B 1084 MET cc_start: 0.2922 (tpt) cc_final: 0.2002 (tpt) REVERT: C 1 MET cc_start: -0.2626 (OUTLIER) cc_final: -0.3452 (ttm) REVERT: D 131 MET cc_start: 0.3715 (mtp) cc_final: 0.2500 (tpt) REVERT: E 1 MET cc_start: 0.0651 (tpt) cc_final: -0.0256 (mtp) REVERT: E 28 TYR cc_start: 0.1927 (m-10) cc_final: 0.1621 (m-10) REVERT: E 93 MET cc_start: 0.0964 (ppp) cc_final: 0.0626 (ppp) REVERT: E 168 TYR cc_start: 0.4756 (m-80) cc_final: 0.4468 (m-80) REVERT: F 151 LEU cc_start: 0.1008 (OUTLIER) cc_final: 0.0386 (pp) REVERT: G 114 MET cc_start: 0.4167 (mpp) cc_final: 0.2976 (mmp) REVERT: J 49 MET cc_start: 0.3918 (tpt) cc_final: 0.3066 (ttm) REVERT: K 142 MET cc_start: 0.1677 (mtm) cc_final: 0.0463 (mmt) REVERT: M 179 LEU cc_start: 0.1117 (OUTLIER) cc_final: 0.0414 (mt) REVERT: N 297 MET cc_start: -0.2247 (mmt) cc_final: -0.3890 (mtt) REVERT: N 305 MET cc_start: -0.0180 (mtm) cc_final: -0.0567 (ttm) REVERT: O 35 SER cc_start: 0.5073 (OUTLIER) cc_final: 0.4667 (t) REVERT: O 327 ARG cc_start: 0.3171 (ttp80) cc_final: 0.2400 (ttt180) REVERT: O 598 GLU cc_start: 0.2971 (mt-10) cc_final: 0.1687 (tt0) REVERT: P 172 ILE cc_start: 0.6011 (tp) cc_final: 0.5438 (tp) REVERT: Q 75 MET cc_start: 0.0744 (mmt) cc_final: -0.0059 (mmm) outliers start: 97 outliers final: 61 residues processed: 479 average time/residue: 0.2510 time to fit residues: 203.1299 Evaluate side-chains 391 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 322 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 936 ASN Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 132 TYR Chi-restraints excluded: chain O residue 209 THR Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain O residue 581 LEU Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 78 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 22 optimal weight: 0.6980 chunk 387 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 238 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 460 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 321 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 GLN A 707 ASN A 936 ASN ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 441 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN B 821 HIS ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.261922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.247022 restraints weight = 65182.185| |-----------------------------------------------------------------------------| r_work (start): 0.4661 rms_B_bonded: 1.10 r_work: 0.4459 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4466 r_free = 0.4466 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4466 r_free = 0.4466 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.4466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2717 moved from start: 0.7556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 41369 Z= 0.153 Angle : 0.795 15.146 56036 Z= 0.402 Chirality : 0.047 0.239 6312 Planarity : 0.006 0.104 7090 Dihedral : 11.168 80.722 5910 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.75 % Favored : 85.09 % Rotamer: Outliers : 1.66 % Allowed : 17.16 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.21 % 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: -3.79 (0.11), residues: 4965 helix: -1.29 (0.13), residues: 1529 sheet: -2.76 (0.23), residues: 403 loop : -3.34 (0.10), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 119 TYR 0.027 0.002 TYR I 31 PHE 0.069 0.002 PHE B 185 TRP 0.031 0.002 TRP A 197 HIS 0.013 0.002 HIS O 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (41361) covalent geometry : angle 0.79534 / 0.40 (56036) hydrogen bonds : bond 0.03489 / 2.45 ( 908) hydrogen bonds : angle 5.16453 / 3.55 ( 2571) metal coordination : bond 0.00196 / 0.10 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9340.12 seconds wall clock time: 161 minutes 34.05 seconds (9694.05 seconds total)