Starting phenix.real_space_refine on Tue Aug 26 19:07:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6eu1_3956/08_2025/6eu1_3956_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6eu1_3956/08_2025/6eu1_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 { model { file = "/net/cci-nas-00/data/ceres_data/6eu1_3956/08_2025/6eu1_3956_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6eu1_3956/08_2025/6eu1_3956_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6eu1_3956/08_2025/6eu1_3956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6eu1_3956/08_2025/6eu1_3956.map" } 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-2.0-5787/lib/python3.9/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: 9.26, per 1000 atoms: 0.23 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: 3.38 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.97 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: 10.69 Time building geometry restraints manager: 4.58 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=" 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 bond pdb=" C VAL E 124 " pdb=" N PRO E 125 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.84e+00 ... (remaining 41356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 55111 3.76 - 7.52: 783 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: 5251 0.078 - 0.156: 901 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 43.360 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0154 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= 0.300 Angle : 1.135 18.809 56036 Z= 0.593 Chirality : 0.062 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 aren 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 covalent geometry : bond 0.00476 (41361) covalent geometry : angle 1.13542 (56036) hydrogen bonds : bond 0.25896 ( 908) hydrogen bonds : angle 9.12674 ( 2571) metal coordination : bond 0.39907 ( 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 : 1.195 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: 0.2406 (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: 0.0807 (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: 0.2168 time to fit residues: 191.8275 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 : 1.237 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 315 HIS A 328 ASN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 648 ASN A 808 GLN A 828 GLN A 838 ASN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 ASN A1131 ASN A1185 GLN A1261 GLN A1318 HIS B 61 HIS ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 244 HIS B 286 ASN B 334 HIS B 552 ASN B 574 GLN B 600 HIS ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN B 821 HIS B 840 GLN B 883 GLN B 891 ASN B 902 GLN B 903 ASN B 970 ASN B1049 GLN B1077 GLN B1130 GLN B1148 GLN C 10 ASN C 29 ASN C 65 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN D 52 HIS D 71 ASN D 125 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 54 GLN E 99 HIS E 104 ASN E 114 ASN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 36 ASN G 69 ASN G 176 ASN H 3 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 HIS O 225 ASN O 295 GLN ** 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 P 258 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.240056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.216851 restraints weight = 61665.596| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.72 r_work: 0.4162 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0828 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41369 Z= 0.158 Angle : 0.775 14.296 56036 Z= 0.399 Chirality : 0.046 0.206 6312 Planarity : 0.006 0.076 7090 Dihedral : 11.436 83.318 5926 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.11 % Favored : 84.63 % Rotamer: Outliers : 2.37 % Allowed : 10.23 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.36 % 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 aren not related in a simple way. whole: -4.81 (0.10), residues: 4965 helix: -2.67 (0.11), residues: 1506 sheet: -2.82 (0.23), residues: 404 loop : -3.74 (0.09), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 68 TYR 0.033 0.002 TYR O 132 PHE 0.020 0.002 PHE O 287 TRP 0.017 0.002 TRP J 18 HIS 0.011 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00334 (41361) covalent geometry : angle 0.77488 (56036) hydrogen bonds : bond 0.04090 ( 908) hydrogen bonds : angle 5.62432 ( 2571) metal coordination : bond 0.00683 ( 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 484 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 380 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.3127 (mm-30) cc_final: 0.2570 (tt0) REVERT: A 540 ASN cc_start: 0.0041 (m-40) cc_final: -0.0221 (m-40) REVERT: A 794 MET cc_start: -0.1521 (tpp) cc_final: -0.2051 (mtt) REVERT: A 1161 VAL cc_start: 0.0857 (p) cc_final: 0.0377 (t) REVERT: A 1291 ARG cc_start: 0.0275 (OUTLIER) cc_final: 0.0020 (ttp-110) REVERT: A 1348 MET cc_start: 0.0796 (mmt) cc_final: -0.1251 (tpp) REVERT: B 286 ASN cc_start: 0.2998 (OUTLIER) cc_final: 0.1264 (m-40) REVERT: B 760 MET cc_start: -0.0586 (OUTLIER) cc_final: -0.1142 (ptm) REVERT: B 1103 TYR cc_start: 0.1961 (p90) cc_final: 0.0020 (p90) REVERT: D 131 MET cc_start: 0.3431 (mtp) cc_final: 0.2274 (tpt) REVERT: E 1 MET cc_start: 0.0229 (tpt) cc_final: -0.0833 (mtp) REVERT: E 197 LYS cc_start: -0.3103 (OUTLIER) cc_final: -0.3310 (ttpm) REVERT: K 142 MET cc_start: 0.2062 (mtm) cc_final: 0.1011 (mmt) REVERT: N 297 MET cc_start: -0.3102 (tpp) cc_final: -0.3717 (ptp) REVERT: O 35 SER cc_start: 0.4566 (OUTLIER) cc_final: 0.4197 (t) REVERT: O 174 TYR cc_start: 0.5550 (t80) cc_final: 0.4942 (t80) REVERT: O 271 LEU cc_start: 0.2267 (OUTLIER) cc_final: 0.1740 (mp) REVERT: O 287 PHE cc_start: 0.3169 (t80) cc_final: 0.2925 (p90) REVERT: O 326 ILE cc_start: 0.1684 (OUTLIER) cc_final: 0.0729 (tt) REVERT: P 166 THR cc_start: 0.2747 (p) cc_final: 0.2536 (m) REVERT: P 299 MET cc_start: 0.4161 (pmm) cc_final: 0.3622 (ptt) outliers start: 104 outliers final: 42 residues processed: 464 average time/residue: 0.1997 time to fit residues: 153.9672 Evaluate side-chains 348 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR 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 500 LEU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 944 ASN 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 61 HIS Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 760 MET Chi-restraints excluded: chain B residue 889 SER 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 87 SER Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain M residue 76 LEU 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 516 LEU Chi-restraints excluded: chain O residue 645 LEU Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 204 optimal weight: 0.9990 chunk 388 optimal weight: 2.9990 chunk 321 optimal weight: 0.0030 chunk 102 optimal weight: 0.0170 chunk 417 optimal weight: 7.9990 chunk 317 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 271 optimal weight: 0.0770 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS A 648 ASN ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 GLN B 61 HIS ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** D 126 GLN ** 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** ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN O 108 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** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.242900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.220651 restraints weight = 67974.515| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.76 r_work: 0.4213 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4215 r_free = 0.4215 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4215 r_free = 0.4215 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0908 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 41369 Z= 0.124 Angle : 0.710 11.769 56036 Z= 0.361 Chirality : 0.045 0.220 6312 Planarity : 0.005 0.085 7090 Dihedral : 11.143 82.868 5918 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.91 % Favored : 84.89 % Rotamer: Outliers : 2.37 % Allowed : 12.71 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % 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 aren not related in a simple way. whole: -4.26 (0.10), residues: 4965 helix: -1.96 (0.12), residues: 1508 sheet: -2.44 (0.25), residues: 395 loop : -3.56 (0.10), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 73 TYR 0.028 0.001 TYR O 494 PHE 0.021 0.001 PHE O 345 TRP 0.023 0.001 TRP O 648 HIS 0.016 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00258 (41361) covalent geometry : angle 0.71010 (56036) hydrogen bonds : bond 0.03539 ( 908) hydrogen bonds : angle 5.03895 ( 2571) metal coordination : bond 0.00447 ( 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 434 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 330 time to evaluate : 1.055 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 274 MET cc_start: 0.2887 (mmt) cc_final: 0.2558 (mmt) REVERT: A 313 MET cc_start: 0.5028 (ppp) cc_final: 0.3098 (mmp) REVERT: A 326 TYR cc_start: 0.3374 (t80) cc_final: 0.2864 (t80) REVERT: A 540 ASN cc_start: -0.0027 (m-40) cc_final: -0.0271 (m-40) REVERT: A 1161 VAL cc_start: 0.0663 (p) cc_final: 0.0203 (t) REVERT: A 1174 GLN cc_start: 0.4598 (tm-30) cc_final: 0.4276 (pp30) REVERT: A 1343 MET cc_start: 0.1881 (mmt) cc_final: 0.1391 (ttm) REVERT: A 1348 MET cc_start: 0.0680 (mmt) cc_final: -0.0628 (tpp) REVERT: A 1421 MET cc_start: 0.3153 (mpp) cc_final: 0.2544 (ptp) REVERT: B 283 PHE cc_start: 0.1768 (t80) cc_final: 0.1007 (t80) REVERT: B 695 GLN cc_start: -0.0985 (OUTLIER) cc_final: -0.2045 (pt0) REVERT: B 735 MET cc_start: 0.1053 (ptm) cc_final: -0.0375 (mmt) REVERT: B 760 MET cc_start: -0.0689 (ptm) cc_final: -0.1017 (ptm) REVERT: B 1103 TYR cc_start: 0.2241 (p90) cc_final: 0.0076 (p90) REVERT: D 131 MET cc_start: 0.3318 (mtp) cc_final: 0.2126 (tpt) REVERT: E 1 MET cc_start: 0.0094 (tpt) cc_final: -0.0970 (mtt) REVERT: F 85 MET cc_start: 0.0113 (mmm) cc_final: -0.1451 (ppp) REVERT: F 151 LEU cc_start: 0.1373 (OUTLIER) cc_final: 0.0999 (pp) REVERT: K 142 MET cc_start: 0.1671 (mtm) cc_final: 0.0861 (mmt) REVERT: O 137 ILE cc_start: 0.1406 (OUTLIER) cc_final: 0.1172 (tp) REVERT: O 139 GLU cc_start: 0.5553 (mm-30) cc_final: 0.4715 (tt0) REVERT: O 140 ILE cc_start: 0.4814 (mt) cc_final: 0.4423 (mt) REVERT: O 145 ARG cc_start: 0.4473 (tpp80) cc_final: 0.3630 (ttm-80) REVERT: O 174 TYR cc_start: 0.5633 (t80) cc_final: 0.4883 (t80) REVERT: O 190 LEU cc_start: 0.3299 (OUTLIER) cc_final: 0.2978 (tt) REVERT: O 271 LEU cc_start: 0.2413 (OUTLIER) cc_final: 0.1920 (mp) REVERT: P 172 ILE cc_start: 0.5711 (tp) cc_final: 0.5127 (tp) REVERT: P 299 MET cc_start: 0.4123 (pmm) cc_final: 0.3622 (ptt) REVERT: Q 39 ILE cc_start: 0.4331 (tp) cc_final: 0.3813 (mp) outliers start: 104 outliers final: 49 residues processed: 407 average time/residue: 0.2062 time to fit residues: 141.9478 Evaluate side-chains 343 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 289 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL 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 848 VAL Chi-restraints excluded: chain A residue 943 TYR 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 133 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 290 SER 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 954 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain E residue 87 SER 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 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 G residue 97 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 137 ILE 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 516 LEU Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 230 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 397 optimal weight: 7.9990 chunk 24 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 449 optimal weight: 1.9990 chunk 478 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 374 optimal weight: 0.0980 chunk 362 optimal weight: 0.9990 chunk 381 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 242 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.247515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.226549 restraints weight = 69572.444| |-----------------------------------------------------------------------------| r_work (start): 0.4472 rms_B_bonded: 1.69 r_work: 0.4248 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4252 r_free = 0.4252 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 = 0.4252 r_free = 0.4252 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1325 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41369 Z= 0.135 Angle : 0.714 13.943 56036 Z= 0.362 Chirality : 0.045 0.225 6312 Planarity : 0.005 0.086 7090 Dihedral : 10.968 78.221 5916 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.37 % Favored : 84.47 % Rotamer: Outliers : 2.67 % Allowed : 13.94 % Favored : 83.39 % 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 aren not related in a simple way. whole: -3.94 (0.11), residues: 4965 helix: -1.50 (0.13), residues: 1494 sheet: -2.50 (0.25), residues: 406 loop : -3.42 (0.10), residues: 3065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 303 TYR 0.022 0.001 TYR O 494 PHE 0.019 0.002 PHE M 162 TRP 0.019 0.002 TRP A 495 HIS 0.039 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00289 (41361) covalent geometry : angle 0.71395 (56036) hydrogen bonds : bond 0.03212 ( 908) hydrogen bonds : angle 4.84075 ( 2571) metal coordination : bond 0.00321 ( 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 441 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 324 time to evaluate : 1.238 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: A 140 ILE cc_start: -0.1899 (OUTLIER) cc_final: -0.2459 (mp) REVERT: A 313 MET cc_start: 0.5169 (ppp) cc_final: 0.3363 (mmp) REVERT: A 794 MET cc_start: -0.1560 (tpp) cc_final: -0.3487 (mtt) REVERT: A 849 ARG cc_start: 0.1785 (OUTLIER) cc_final: 0.1030 (tpp-160) REVERT: A 1032 LEU cc_start: 0.0768 (OUTLIER) cc_final: 0.0499 (mm) REVERT: A 1174 GLN cc_start: 0.4267 (tm-30) cc_final: 0.4021 (tt0) REVERT: A 1348 MET cc_start: 0.0888 (mmt) cc_final: -0.0341 (tpp) REVERT: B 590 ILE cc_start: -0.1748 (OUTLIER) cc_final: -0.2083 (mp) REVERT: B 695 GLN cc_start: -0.0165 (OUTLIER) cc_final: -0.1229 (pt0) REVERT: B 735 MET cc_start: 0.0957 (ptm) cc_final: 0.0009 (mmt) REVERT: B 760 MET cc_start: -0.0768 (ptm) cc_final: -0.1027 (ptm) REVERT: B 885 MET cc_start: 0.3519 (pmm) cc_final: 0.2777 (pmm) REVERT: B 985 GLU cc_start: 0.6690 (tp30) cc_final: 0.6295 (mm-30) REVERT: B 1084 MET cc_start: 0.3108 (tmm) cc_final: 0.2018 (mtm) REVERT: D 131 MET cc_start: 0.3400 (mtp) cc_final: 0.2454 (tpp) REVERT: D 153 MET cc_start: -0.0432 (mmt) cc_final: -0.0824 (mmm) REVERT: E 1 MET cc_start: -0.0047 (tpt) cc_final: -0.0856 (mtp) REVERT: F 85 MET cc_start: 0.0416 (mmm) cc_final: -0.0424 (tpp) REVERT: F 103 MET cc_start: 0.2118 (tpt) cc_final: 0.1150 (ptt) REVERT: G 115 LEU cc_start: 0.0504 (OUTLIER) cc_final: -0.1248 (tp) REVERT: J 2 ILE cc_start: 0.1531 (mp) cc_final: 0.0388 (mt) REVERT: K 142 MET cc_start: 0.1715 (mtm) cc_final: 0.0783 (mmt) REVERT: M 179 LEU cc_start: 0.0820 (OUTLIER) cc_final: 0.0005 (mt) REVERT: N 297 MET cc_start: -0.2996 (mmt) cc_final: -0.4417 (mtt) REVERT: O 137 ILE cc_start: 0.1508 (OUTLIER) cc_final: 0.1283 (tt) REVERT: O 139 GLU cc_start: 0.5420 (mm-30) cc_final: 0.4963 (tt0) REVERT: O 174 TYR cc_start: 0.5824 (t80) cc_final: 0.5029 (t80) REVERT: O 190 LEU cc_start: 0.3926 (OUTLIER) cc_final: 0.3636 (tt) REVERT: P 172 ILE cc_start: 0.5904 (tp) cc_final: 0.5310 (tp) REVERT: P 299 MET cc_start: 0.3882 (pmm) cc_final: 0.3578 (ptt) outliers start: 117 outliers final: 62 residues processed: 418 average time/residue: 0.2106 time to fit residues: 148.0176 Evaluate side-chains 355 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 284 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 227 THR Chi-restraints excluded: chain A residue 228 LEU 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 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 1032 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1362 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 133 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 VAL 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 756 THR Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1137 ILE 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 321 LEU Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 VAL 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 115 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 117 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 373 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 214 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 O residue 645 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 191 optimal weight: 0.9980 chunk 476 optimal weight: 7.9990 chunk 403 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 459 optimal weight: 4.9990 chunk 416 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN A 815 GLN A 936 ASN A1006 HIS A1131 ASN A1180 ASN A1385 GLN B 60 GLN B 80 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 286 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 HIS ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1148 GLN C 14 ASN C 65 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 232 GLN C 234 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 71 ASN E 99 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN H 133 ASN J 53 HIS M 86 HIS M 89 GLN ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 254 GLN ** O 56 HIS ** 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 295 GLN ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 456 HIS ** O 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 616 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.268608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.256429 restraints weight = 68764.946| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 1.15 r_work: 0.4607 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.4607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4607 r_free = 0.4607 target_work(ls_wunit_k1) = 0.241 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4607 r_free = 0.4607 target_work(ls_wunit_k1) = 0.241 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4425 moved from start: 1.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.235 41369 Z= 0.444 Angle : 1.454 20.359 56036 Z= 0.758 Chirality : 0.072 0.533 6312 Planarity : 0.011 0.129 7090 Dihedral : 13.017 87.908 5912 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 27.38 Ramachandran Plot: Outliers : 0.42 % Allowed : 20.02 % Favored : 79.55 % Rotamer: Outliers : 4.94 % Allowed : 15.13 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.21 (0.09), residues: 4965 helix: -3.02 (0.10), residues: 1478 sheet: -3.17 (0.23), residues: 365 loop : -3.97 (0.09), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG P 262 TYR 0.069 0.006 TYR K 108 PHE 0.057 0.006 PHE F 143 TRP 0.044 0.004 TRP A 495 HIS 0.033 0.005 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.01020 (41361) covalent geometry : angle 1.45434 (56036) hydrogen bonds : bond 0.08124 ( 908) hydrogen bonds : angle 8.22312 ( 2571) metal coordination : bond 0.01125 ( 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 837 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 620 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.2029 (OUTLIER) cc_final: 0.1239 (pp20) REVERT: A 313 MET cc_start: 0.6209 (ppp) cc_final: 0.5112 (mmp) REVERT: A 408 VAL cc_start: 0.6676 (m) cc_final: 0.5799 (t) REVERT: A 470 ASP cc_start: 0.6472 (m-30) cc_final: 0.5914 (m-30) REVERT: A 472 VAL cc_start: 0.6391 (p) cc_final: 0.5284 (t) REVERT: A 583 MET cc_start: 0.6460 (tmm) cc_final: 0.5718 (ppp) REVERT: A 626 LEU cc_start: 0.1892 (OUTLIER) cc_final: 0.1266 (pt) REVERT: A 849 ARG cc_start: 0.4396 (OUTLIER) cc_final: 0.3681 (tpp-160) REVERT: A 1260 MET cc_start: 0.0440 (OUTLIER) cc_final: 0.0182 (mtt) REVERT: A 1291 ARG cc_start: 0.0799 (OUTLIER) cc_final: 0.0518 (ttp80) REVERT: A 1348 MET cc_start: 0.1082 (mmt) cc_final: -0.1283 (ttt) REVERT: A 1360 ASP cc_start: 0.2441 (OUTLIER) cc_final: 0.1345 (m-30) REVERT: A 1369 LEU cc_start: 0.3617 (OUTLIER) cc_final: 0.3309 (tp) REVERT: B 267 GLU cc_start: 0.3940 (OUTLIER) cc_final: 0.3028 (tt0) REVERT: B 314 ARG cc_start: 0.2830 (OUTLIER) cc_final: 0.2030 (mtm180) REVERT: B 325 GLU cc_start: 0.1961 (OUTLIER) cc_final: 0.1697 (tt0) REVERT: B 351 MET cc_start: 0.0705 (ppp) cc_final: 0.0408 (mmt) REVERT: B 382 GLN cc_start: 0.6260 (mm110) cc_final: 0.6050 (mm110) REVERT: B 435 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7230 (mpt-90) REVERT: B 489 LEU cc_start: 0.1841 (OUTLIER) cc_final: 0.1488 (tt) REVERT: B 549 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4035 (tp) REVERT: B 916 HIS cc_start: 0.4738 (OUTLIER) cc_final: 0.4261 (m170) REVERT: B 945 ASN cc_start: 0.5357 (OUTLIER) cc_final: 0.4916 (t0) REVERT: B 1034 LYS cc_start: 0.6123 (mmtp) cc_final: 0.5470 (mttp) REVERT: C 33 VAL cc_start: -0.2645 (OUTLIER) cc_final: -0.2991 (p) REVERT: C 68 ARG cc_start: 0.5015 (ttp80) cc_final: 0.4190 (tmm-80) REVERT: C 197 ARG cc_start: 0.5854 (tpp-160) cc_final: 0.5380 (mpp80) REVERT: D 131 MET cc_start: 0.3922 (mtp) cc_final: 0.3181 (tpt) REVERT: E 1 MET cc_start: 0.1153 (tpt) cc_final: -0.0235 (ptm) REVERT: E 121 MET cc_start: 0.4584 (OUTLIER) cc_final: 0.4194 (ppp) REVERT: F 88 TYR cc_start: 0.7603 (m-80) cc_final: 0.7383 (m-80) REVERT: F 103 MET cc_start: 0.5221 (tpt) cc_final: 0.4890 (tpp) REVERT: F 138 LEU cc_start: 0.5376 (tt) cc_final: 0.5147 (tp) REVERT: K 76 LEU cc_start: 0.3051 (tp) cc_final: 0.2786 (tp) REVERT: M 76 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4720 (tp) REVERT: M 179 LEU cc_start: 0.2403 (OUTLIER) cc_final: 0.1442 (mt) REVERT: N 297 MET cc_start: -0.2378 (mmt) cc_final: -0.3565 (mtt) REVERT: N 380 MET cc_start: 0.4511 (mmt) cc_final: 0.3730 (mmt) REVERT: O 255 LYS cc_start: 0.3297 (tttt) cc_final: 0.2571 (mmmm) REVERT: O 289 LYS cc_start: 0.5525 (OUTLIER) cc_final: 0.4653 (mptt) REVERT: O 456 HIS cc_start: 0.3284 (t70) cc_final: 0.3047 (t70) REVERT: O 484 MET cc_start: 0.2814 (OUTLIER) cc_final: 0.2424 (ptp) REVERT: O 582 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7121 (mm-30) REVERT: O 594 LYS cc_start: 0.6850 (mmtm) cc_final: 0.6021 (tttt) REVERT: O 598 GLU cc_start: 0.4195 (mt-10) cc_final: 0.3809 (mt-10) REVERT: P 172 ILE cc_start: 0.6214 (tp) cc_final: 0.5618 (tp) REVERT: P 250 ASP cc_start: 0.5360 (OUTLIER) cc_final: 0.4916 (p0) REVERT: P 308 GLU cc_start: 0.3200 (OUTLIER) cc_final: 0.2444 (mt-10) REVERT: Q 59 ILE cc_start: 0.7581 (mt) cc_final: 0.7293 (mt) REVERT: Q 63 LYS cc_start: 0.7048 (mtpt) cc_final: 0.6735 (tttt) REVERT: Q 75 MET cc_start: 0.1946 (mmt) cc_final: 0.0630 (mmm) outliers start: 217 outliers final: 78 residues processed: 782 average time/residue: 0.2307 time to fit residues: 293.0022 Evaluate side-chains 535 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 434 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1342 THR Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain A residue 1362 MET Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 916 HIS Chi-restraints excluded: chain B residue 938 ILE Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain F residue 74 ILE 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 G residue 89 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 111 THR 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 N residue 379 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 65 ILE 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 314 ILE 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 O residue 537 LEU Chi-restraints excluded: chain P residue 176 ASN Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 250 ASP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 308 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 456 optimal weight: 1.9990 chunk 203 optimal weight: 0.0970 chunk 200 optimal weight: 0.7980 chunk 403 optimal weight: 10.0000 chunk 383 optimal weight: 0.5980 chunk 419 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 490 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A 692 ASN A 899 GLN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 GLN B 81 GLN B 116 HIS B 286 ASN B 374 ASN B 441 ASN B 558 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 HIS ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 ASN B 800 ASN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS B1148 GLN C 10 ASN C 175 GLN C 207 HIS D 71 ASN E 99 HIS ** E 147 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 N 377 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 197 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.266416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.253317 restraints weight = 70677.483| |-----------------------------------------------------------------------------| r_work (start): 0.4713 rms_B_bonded: 1.11 r_work: 0.4563 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4568 r_free = 0.4568 target_work(ls_wunit_k1) = 0.237 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4568 r_free = 0.4568 target_work(ls_wunit_k1) = 0.237 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4418 moved from start: 1.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 41369 Z= 0.161 Angle : 0.835 12.866 56036 Z= 0.427 Chirality : 0.049 0.259 6312 Planarity : 0.006 0.080 7090 Dihedral : 11.693 84.395 5909 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.71 % Favored : 85.07 % Rotamer: Outliers : 2.89 % Allowed : 18.43 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.36 % 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 aren not related in a simple way. whole: -4.52 (0.10), residues: 4965 helix: -2.19 (0.11), residues: 1502 sheet: -2.79 (0.24), residues: 376 loop : -3.68 (0.09), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 788 TYR 0.029 0.002 TYR I 31 PHE 0.029 0.002 PHE O 576 TRP 0.021 0.002 TRP A 788 HIS 0.023 0.002 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00351 (41361) covalent geometry : angle 0.83539 (56036) hydrogen bonds : bond 0.04037 ( 908) hydrogen bonds : angle 5.92558 ( 2571) metal coordination : bond 0.00210 ( 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 625 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 498 time to evaluate : 1.181 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 312 MET cc_start: 0.5524 (tpp) cc_final: 0.5164 (ttt) REVERT: A 313 MET cc_start: 0.6000 (ppp) cc_final: 0.5164 (mmp) REVERT: A 408 VAL cc_start: 0.6890 (OUTLIER) cc_final: 0.5278 (t) REVERT: A 516 GLU cc_start: 0.7385 (pt0) cc_final: 0.7162 (pt0) REVERT: A 694 MET cc_start: 0.3763 (mpp) cc_final: 0.2927 (mmp) REVERT: A 794 MET cc_start: 0.0573 (tpp) cc_final: -0.0646 (ptp) REVERT: A 849 ARG cc_start: 0.3513 (OUTLIER) cc_final: 0.2374 (tpp-160) REVERT: A 926 MET cc_start: 0.2863 (mmp) cc_final: 0.2572 (mmm) REVERT: A 960 MET cc_start: -0.0319 (OUTLIER) cc_final: -0.1007 (tmm) REVERT: A 1260 MET cc_start: -0.0080 (OUTLIER) cc_final: -0.1196 (ppp) REVERT: A 1291 ARG cc_start: 0.0927 (OUTLIER) cc_final: 0.0571 (ttp80) REVERT: A 1348 MET cc_start: 0.0288 (mmt) cc_final: -0.1614 (ttt) REVERT: A 1357 LEU cc_start: 0.4849 (tt) cc_final: 0.4008 (tp) REVERT: A 1380 ARG cc_start: 0.5337 (tpp-160) cc_final: 0.5055 (tpt170) REVERT: B 109 LYS cc_start: 0.5094 (mmtm) cc_final: 0.4548 (mmtt) REVERT: B 269 MET cc_start: 0.2225 (tpt) cc_final: 0.0487 (ppp) REVERT: B 314 ARG cc_start: 0.2556 (OUTLIER) cc_final: 0.2056 (mtm180) REVERT: B 930 ASP cc_start: 0.4327 (m-30) cc_final: 0.4044 (p0) REVERT: C 132 ILE cc_start: 0.7744 (mp) cc_final: 0.7511 (mt) REVERT: C 197 ARG cc_start: 0.6252 (tpp-160) cc_final: 0.5937 (mpp80) REVERT: D 48 ARG cc_start: 0.3798 (OUTLIER) cc_final: 0.1707 (ttt-90) REVERT: D 131 MET cc_start: 0.4075 (mtp) cc_final: 0.2938 (tpt) REVERT: D 153 MET cc_start: 0.0339 (mmm) cc_final: -0.0020 (mmm) REVERT: E 1 MET cc_start: 0.1093 (tpt) cc_final: -0.0287 (ptm) REVERT: E 50 MET cc_start: 0.1838 (ppp) cc_final: 0.1454 (ppp) REVERT: E 121 MET cc_start: 0.4800 (ppp) cc_final: 0.4460 (ptt) REVERT: E 215 MET cc_start: 0.5374 (mtp) cc_final: 0.5070 (mtm) REVERT: F 88 TYR cc_start: 0.7349 (m-80) cc_final: 0.6915 (m-10) REVERT: F 144 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6461 (mt-10) REVERT: G 29 GLN cc_start: 0.6809 (tp-100) cc_final: 0.6576 (mm-40) REVERT: G 111 PRO cc_start: 0.3913 (Cg_exo) cc_final: 0.3674 (Cg_endo) REVERT: K 41 GLU cc_start: 0.3895 (tm-30) cc_final: 0.2911 (mp0) REVERT: K 81 MET cc_start: 0.2318 (ttp) cc_final: 0.1450 (ttp) REVERT: M 107 ILE cc_start: 0.1887 (OUTLIER) cc_final: 0.1679 (mp) REVERT: M 179 LEU cc_start: 0.1825 (OUTLIER) cc_final: 0.1474 (mt) REVERT: N 297 MET cc_start: -0.1867 (mmt) cc_final: -0.4934 (pmm) REVERT: N 364 ARG cc_start: 0.3316 (ptm-80) cc_final: 0.2546 (mtm-85) REVERT: N 380 MET cc_start: 0.3928 (mmt) cc_final: 0.2213 (ttt) REVERT: O 67 MET cc_start: 0.5079 (mmm) cc_final: 0.4826 (mmp) REVERT: O 197 MET cc_start: 0.2648 (tmm) cc_final: 0.2188 (tmm) REVERT: O 255 LYS cc_start: 0.3087 (tttt) cc_final: 0.2571 (mmmm) REVERT: O 289 LYS cc_start: 0.5496 (OUTLIER) cc_final: 0.4747 (mptt) REVERT: O 598 GLU cc_start: 0.3693 (mt-10) cc_final: 0.3243 (tt0) REVERT: P 172 ILE cc_start: 0.5821 (tp) cc_final: 0.5305 (tp) REVERT: Q 63 LYS cc_start: 0.6745 (mtpt) cc_final: 0.6531 (ttpt) REVERT: Q 75 MET cc_start: 0.1593 (mmt) cc_final: 0.0240 (mmm) outliers start: 127 outliers final: 48 residues processed: 589 average time/residue: 0.2103 time to fit residues: 204.7998 Evaluate side-chains 462 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 404 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1291 ARG Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 847 VAL Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 336 LEU 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 304 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 412 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 236 optimal weight: 0.7980 chunk 386 optimal weight: 4.9990 chunk 176 optimal weight: 0.1980 chunk 466 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 482 optimal weight: 0.0060 chunk 479 optimal weight: 5.9990 chunk 266 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 HIS B 188 ASN B 286 ASN B 298 GLN ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN B 800 ASN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 232 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS ** M 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN N 366 HIS O 123 ASN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.263821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.249917 restraints weight = 78329.323| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 1.39 r_work: 0.4549 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4554 r_free = 0.4554 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4554 r_free = 0.4554 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4479 moved from start: 1.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41369 Z= 0.152 Angle : 0.781 12.430 56036 Z= 0.397 Chirality : 0.047 0.235 6312 Planarity : 0.006 0.076 7090 Dihedral : 11.241 83.741 5908 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.89 % Favored : 83.94 % Rotamer: Outliers : 2.26 % Allowed : 18.77 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.36 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.15 (0.10), residues: 4965 helix: -1.72 (0.12), residues: 1515 sheet: -2.50 (0.24), residues: 408 loop : -3.56 (0.10), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 6 TYR 0.040 0.002 TYR B 371 PHE 0.033 0.002 PHE A 40 TRP 0.025 0.002 TRP A 788 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00320 (41361) covalent geometry : angle 0.78084 (56036) hydrogen bonds : bond 0.03517 ( 908) hydrogen bonds : angle 5.28273 ( 2571) metal coordination : bond 0.01686 ( 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 560 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 461 time to evaluate : 1.183 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: 0.1627 (OUTLIER) cc_final: 0.0872 (pp20) REVERT: A 313 MET cc_start: 0.6105 (ppp) cc_final: 0.5369 (mmp) REVERT: A 408 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.6436 (t) REVERT: A 694 MET cc_start: 0.3071 (mpp) cc_final: 0.1772 (ptp) REVERT: A 794 MET cc_start: 0.0552 (tpp) cc_final: -0.0320 (ptp) REVERT: A 1260 MET cc_start: 0.0849 (OUTLIER) cc_final: -0.0402 (ppp) REVERT: A 1348 MET cc_start: 0.0201 (mmt) cc_final: -0.1728 (ttt) REVERT: A 1380 ARG cc_start: 0.5793 (tpp-160) cc_final: 0.5553 (mmp-170) REVERT: B 269 MET cc_start: 0.2011 (tpt) cc_final: 0.0740 (ppp) REVERT: B 314 ARG cc_start: 0.3492 (OUTLIER) cc_final: 0.2935 (mtm180) REVERT: B 358 MET cc_start: -0.1077 (mmp) cc_final: -0.2368 (ptt) REVERT: B 470 MET cc_start: 0.7290 (mmt) cc_final: 0.6699 (mmt) REVERT: B 695 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6582 (pp30) REVERT: B 786 GLU cc_start: 0.7024 (tt0) cc_final: 0.5751 (tt0) REVERT: B 1003 MET cc_start: 0.4700 (tmm) cc_final: 0.3489 (tpp) REVERT: C 1 MET cc_start: -0.2691 (mtt) cc_final: -0.3769 (ttm) REVERT: D 131 MET cc_start: 0.4272 (mtp) cc_final: 0.3588 (tpt) REVERT: E 1 MET cc_start: 0.1039 (tpt) cc_final: -0.0159 (ptm) REVERT: E 50 MET cc_start: 0.1704 (ppp) cc_final: 0.1386 (ppp) REVERT: F 144 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6637 (mt-10) REVERT: G 168 LEU cc_start: 0.0578 (tp) cc_final: 0.0275 (mt) REVERT: K 81 MET cc_start: 0.2795 (ttp) cc_final: 0.1631 (ttp) REVERT: K 142 MET cc_start: 0.3429 (mpp) cc_final: 0.1080 (mmt) REVERT: N 297 MET cc_start: -0.1121 (mmt) cc_final: -0.4310 (pmm) REVERT: N 366 HIS cc_start: 0.2164 (OUTLIER) cc_final: 0.1664 (m-70) REVERT: N 380 MET cc_start: 0.3881 (mmt) cc_final: 0.2514 (ttt) REVERT: O 197 MET cc_start: 0.2512 (tmm) cc_final: 0.2159 (tmm) REVERT: P 172 ILE cc_start: 0.6005 (tp) cc_final: 0.5482 (tp) REVERT: P 258 HIS cc_start: 0.3785 (OUTLIER) cc_final: 0.2183 (m-70) REVERT: P 299 MET cc_start: 0.4628 (ppp) cc_final: 0.3333 (ptm) REVERT: Q 75 MET cc_start: 0.1407 (mmt) cc_final: 0.0301 (mmm) outliers start: 99 outliers final: 48 residues processed: 533 average time/residue: 0.1936 time to fit residues: 173.2927 Evaluate side-chains 447 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 392 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 695 GLN Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 366 HIS Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 258 HIS Chi-restraints excluded: chain P residue 263 VAL 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: 5.9990 chunk 371 optimal weight: 0.6980 chunk 393 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 361 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 70 optimal weight: 0.0060 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS B 286 ASN B 425 HIS ** B 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 HIS ** B 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS D 51 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS M 89 GLN ** 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 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.261011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.246745 restraints weight = 68684.946| |-----------------------------------------------------------------------------| r_work (start): 0.4665 rms_B_bonded: 1.30 r_work: 0.4521 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4520 r_free = 0.4520 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4520 r_free = 0.4520 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4782 moved from start: 1.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 41369 Z= 0.155 Angle : 0.787 12.568 56036 Z= 0.400 Chirality : 0.048 0.355 6312 Planarity : 0.006 0.079 7090 Dihedral : 11.077 83.107 5908 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.54 % Favored : 85.29 % Rotamer: Outliers : 2.10 % Allowed : 19.28 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.36 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.88 (0.11), residues: 4965 helix: -1.42 (0.13), residues: 1538 sheet: -2.37 (0.25), residues: 411 loop : -3.45 (0.10), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 130 TYR 0.028 0.002 TYR Q 58 PHE 0.027 0.002 PHE A 40 TRP 0.025 0.002 TRP A 788 HIS 0.023 0.002 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00345 (41361) covalent geometry : angle 0.78746 (56036) hydrogen bonds : bond 0.03487 ( 908) hydrogen bonds : angle 5.10058 ( 2571) metal coordination : bond 0.00389 ( 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 547 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 455 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.1503 (OUTLIER) cc_final: 0.0811 (pp20) REVERT: A 55 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6026 (m-30) REVERT: A 313 MET cc_start: 0.6091 (ppp) cc_final: 0.5548 (mmp) REVERT: A 391 GLU cc_start: 0.7086 (tt0) cc_final: 0.6873 (tt0) REVERT: A 403 THR cc_start: 0.8351 (m) cc_final: 0.8105 (p) REVERT: A 408 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.6220 (t) REVERT: A 580 LEU cc_start: 0.7925 (mm) cc_final: 0.7598 (mt) REVERT: A 583 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7010 (ppp) REVERT: A 694 MET cc_start: 0.3608 (mpp) cc_final: 0.3080 (ttp) REVERT: A 794 MET cc_start: 0.0715 (tpp) cc_final: -0.0285 (ptp) REVERT: A 890 MET cc_start: 0.7169 (tpp) cc_final: 0.6659 (tpt) REVERT: A 1348 MET cc_start: 0.0029 (mmt) cc_final: -0.1657 (ttt) REVERT: A 1371 ILE cc_start: 0.5324 (OUTLIER) cc_final: 0.4347 (mm) REVERT: B 269 MET cc_start: 0.2220 (tpt) cc_final: 0.0832 (ppp) REVERT: B 314 ARG cc_start: 0.3391 (OUTLIER) cc_final: 0.2962 (mtm180) REVERT: B 358 MET cc_start: -0.0524 (mmp) cc_final: -0.1599 (ptt) REVERT: B 420 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4732 (tp) REVERT: B 435 ARG cc_start: 0.7682 (mpt-90) cc_final: 0.7347 (mtt90) REVERT: B 496 MET cc_start: 0.3396 (tpt) cc_final: 0.2483 (mtm) REVERT: B 873 TYR cc_start: 0.8254 (t80) cc_final: 0.7704 (t80) REVERT: B 955 VAL cc_start: 0.8772 (m) cc_final: 0.8522 (t) REVERT: C 1 MET cc_start: -0.1711 (mtt) cc_final: -0.3450 (ttm) REVERT: C 308 MET cc_start: 0.6134 (mpp) cc_final: 0.5893 (mtm) REVERT: D 131 MET cc_start: 0.4547 (mtp) cc_final: 0.3254 (tpt) REVERT: E 1 MET cc_start: 0.1345 (tpt) cc_final: 0.0145 (ptm) REVERT: E 50 MET cc_start: 0.1293 (ppp) cc_final: 0.0880 (ppp) REVERT: E 57 MET cc_start: 0.4563 (tpt) cc_final: 0.3468 (ptp) REVERT: F 89 GLU cc_start: 0.6396 (pm20) cc_final: 0.5629 (mp0) REVERT: F 144 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6691 (mt-10) REVERT: G 89 ILE cc_start: 0.2635 (OUTLIER) cc_final: 0.2243 (mt) REVERT: G 105 PHE cc_start: 0.2367 (OUTLIER) cc_final: 0.1913 (t80) REVERT: K 81 MET cc_start: 0.3660 (ttp) cc_final: 0.3327 (mmm) REVERT: K 142 MET cc_start: 0.3828 (mpp) cc_final: 0.1436 (mmt) REVERT: N 297 MET cc_start: -0.1354 (mmt) cc_final: -0.4594 (pmm) REVERT: N 380 MET cc_start: 0.3922 (mmt) cc_final: 0.2636 (ttt) REVERT: O 197 MET cc_start: 0.2994 (tmm) cc_final: 0.2642 (tmm) REVERT: O 577 MET cc_start: 0.8310 (tpp) cc_final: 0.7860 (ttp) REVERT: P 172 ILE cc_start: 0.5762 (tp) cc_final: 0.5305 (tp) REVERT: P 299 MET cc_start: 0.4674 (ppp) cc_final: 0.3280 (ptm) REVERT: Q 75 MET cc_start: 0.1276 (mmt) cc_final: 0.0226 (mmm) outliers start: 92 outliers final: 48 residues processed: 521 average time/residue: 0.1960 time to fit residues: 171.3373 Evaluate side-chains 455 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 398 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 287 HIS Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 240 ILE Chi-restraints excluded: chain P residue 304 LYS Chi-restraints excluded: chain P residue 308 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 35 optimal weight: 0.6980 chunk 292 optimal weight: 9.9990 chunk 375 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 134 optimal weight: 0.0070 chunk 350 optimal weight: 0.6980 chunk 309 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 342 optimal weight: 8.9990 chunk 457 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS A 481 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 234 ASN D 71 ASN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 366 HIS N 377 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.255553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.239974 restraints weight = 75949.772| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 1.46 r_work: 0.4479 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.4425 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4429 r_free = 0.4429 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4429 r_free = 0.4429 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5294 moved from start: 1.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 41369 Z= 0.182 Angle : 0.847 15.775 56036 Z= 0.426 Chirality : 0.050 0.503 6312 Planarity : 0.006 0.075 7090 Dihedral : 11.080 84.435 5908 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.40 % Favored : 83.48 % Rotamer: Outliers : 2.55 % Allowed : 19.62 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.82 (0.11), residues: 4965 helix: -1.37 (0.13), residues: 1538 sheet: -2.34 (0.24), residues: 426 loop : -3.41 (0.10), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 87 TYR 0.032 0.002 TYR Q 58 PHE 0.032 0.002 PHE A 474 TRP 0.039 0.002 TRP B 442 HIS 0.010 0.002 HIS N 366 Details of bonding type rmsd covalent geometry : bond 0.00413 (41361) covalent geometry : angle 0.84699 (56036) hydrogen bonds : bond 0.03790 ( 908) hydrogen bonds : angle 5.23853 ( 2571) metal coordination : bond 0.00411 ( 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 653 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 541 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.4362 (mtmt) cc_final: 0.3667 (pttp) REVERT: A 60 VAL cc_start: 0.7360 (t) cc_final: 0.7084 (m) REVERT: A 299 ILE cc_start: 0.7741 (mm) cc_final: 0.7505 (mm) REVERT: A 403 THR cc_start: 0.8554 (m) cc_final: 0.8316 (p) REVERT: A 685 TYR cc_start: 0.7702 (m-80) cc_final: 0.7456 (m-80) REVERT: A 697 MET cc_start: 0.4308 (mmt) cc_final: 0.4067 (tpp) REVERT: A 794 MET cc_start: 0.1571 (tpp) cc_final: 0.0278 (ptp) REVERT: A 809 MET cc_start: 0.5358 (mmp) cc_final: 0.4752 (mtt) REVERT: A 890 MET cc_start: 0.7600 (tpp) cc_final: 0.7247 (tpt) REVERT: A 1032 LEU cc_start: -0.0276 (OUTLIER) cc_final: -0.0518 (tp) REVERT: A 1126 ILE cc_start: 0.7465 (tp) cc_final: 0.7191 (tp) REVERT: A 1348 MET cc_start: 0.0118 (mmt) cc_final: -0.1343 (ttm) REVERT: A 1379 MET cc_start: 0.2398 (mmm) cc_final: 0.1592 (tmm) REVERT: B 269 MET cc_start: 0.2459 (tpt) cc_final: 0.1060 (ppp) REVERT: B 358 MET cc_start: 0.0208 (mmp) cc_final: -0.0693 (ptt) REVERT: B 420 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5322 (tp) REVERT: B 435 ARG cc_start: 0.7841 (mpt-90) cc_final: 0.7622 (mtt90) REVERT: B 496 MET cc_start: 0.3708 (tpt) cc_final: 0.2918 (mtt) REVERT: B 586 GLU cc_start: 0.5213 (tm-30) cc_final: 0.4145 (tm-30) REVERT: B 873 TYR cc_start: 0.8434 (t80) cc_final: 0.8107 (t80) REVERT: B 958 MET cc_start: 0.3898 (tpp) cc_final: 0.3660 (mpp) REVERT: C 1 MET cc_start: -0.1637 (mtt) cc_final: -0.3407 (ttm) REVERT: C 71 MET cc_start: 0.8807 (tpp) cc_final: 0.8067 (mtt) REVERT: C 222 VAL cc_start: 0.7920 (t) cc_final: 0.7715 (m) REVERT: E 1 MET cc_start: 0.1736 (tpt) cc_final: 0.0517 (ptm) REVERT: E 50 MET cc_start: 0.1140 (OUTLIER) cc_final: 0.0587 (ppp) REVERT: F 89 GLU cc_start: 0.7493 (pm20) cc_final: 0.6634 (mp0) REVERT: F 144 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7653 (tp30) REVERT: G 89 ILE cc_start: 0.3186 (OUTLIER) cc_final: 0.2869 (mt) REVERT: G 105 PHE cc_start: 0.2301 (OUTLIER) cc_final: -0.0101 (t80) REVERT: G 205 MET cc_start: 0.4043 (mpp) cc_final: 0.3689 (mtm) REVERT: H 102 TYR cc_start: 0.2795 (p90) cc_final: 0.2040 (p90) REVERT: K 99 ASN cc_start: 0.7878 (p0) cc_final: 0.7659 (p0) REVERT: K 133 SER cc_start: 0.6120 (m) cc_final: 0.5642 (p) REVERT: K 142 MET cc_start: 0.4020 (mpp) cc_final: 0.1982 (mmt) REVERT: N 297 MET cc_start: -0.1368 (mmt) cc_final: -0.2881 (mtt) REVERT: N 380 MET cc_start: 0.4220 (mmt) cc_final: 0.3099 (ttt) REVERT: O 137 ILE cc_start: 0.7033 (pp) cc_final: 0.6823 (pt) REVERT: O 293 SER cc_start: 0.7372 (p) cc_final: 0.6752 (m) REVERT: O 527 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4845 (tp) REVERT: O 546 VAL cc_start: 0.4685 (OUTLIER) cc_final: 0.3611 (p) REVERT: O 577 MET cc_start: 0.8417 (tpp) cc_final: 0.8164 (ttp) REVERT: P 172 ILE cc_start: 0.5776 (tp) cc_final: 0.5368 (tp) REVERT: P 195 PHE cc_start: 0.4141 (m-80) cc_final: 0.3937 (m-80) REVERT: P 299 MET cc_start: 0.4605 (ppp) cc_final: 0.3741 (ptm) REVERT: Q 75 MET cc_start: 0.1428 (mmt) cc_final: 0.0606 (mmm) outliers start: 112 outliers final: 69 residues processed: 622 average time/residue: 0.2018 time to fit residues: 210.0260 Evaluate side-chains 520 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 444 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1429 LYS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 117 HIS Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 287 HIS Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 336 LEU Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain O residue 546 VAL Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 308 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 182 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 462 optimal weight: 9.9990 chunk 324 optimal weight: 0.0870 chunk 478 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 343 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 466 optimal weight: 0.0770 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 533 ASN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 800 ASN B 902 GLN B 916 HIS B1049 GLN C 93 GLN E 114 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS ** M 86 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** M 254 GLN N 377 ASN ** O 43 ASN ** 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 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 549 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 = 0.4750 r_free = 0.4750 target = 0.255796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.241003 restraints weight = 75322.411| |-----------------------------------------------------------------------------| r_work (start): 0.4620 rms_B_bonded: 1.43 r_work: 0.4483 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work: 0.4436 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4438 r_free = 0.4438 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4438 r_free = 0.4438 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 moved from start: 1.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41369 Z= 0.138 Angle : 0.790 20.804 56036 Z= 0.394 Chirality : 0.047 0.309 6312 Planarity : 0.005 0.076 7090 Dihedral : 10.936 83.238 5908 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.88 % Favored : 85.98 % Rotamer: Outliers : 1.80 % Allowed : 20.64 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.36 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.59 (0.11), residues: 4965 helix: -1.09 (0.13), residues: 1533 sheet: -2.21 (0.25), residues: 423 loop : -3.32 (0.10), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 47 TYR 0.030 0.002 TYR Q 58 PHE 0.028 0.002 PHE A 40 TRP 0.027 0.002 TRP B 442 HIS 0.006 0.001 HIS B1036 Details of bonding type rmsd covalent geometry : bond 0.00309 (41361) covalent geometry : angle 0.78987 (56036) hydrogen bonds : bond 0.03256 ( 908) hydrogen bonds : angle 5.00249 ( 2571) metal coordination : bond 0.00224 ( 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 577 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 498 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.4501 (mtmt) cc_final: 0.3837 (pttp) REVERT: A 60 VAL cc_start: 0.7211 (t) cc_final: 0.7003 (m) REVERT: A 288 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7445 (mmtt) REVERT: A 299 ILE cc_start: 0.7640 (mm) cc_final: 0.7401 (mm) REVERT: A 403 THR cc_start: 0.8552 (m) cc_final: 0.8257 (p) REVERT: A 517 MET cc_start: 0.7564 (ptt) cc_final: 0.7290 (ptt) REVERT: A 576 LEU cc_start: 0.7936 (tp) cc_final: 0.7620 (tt) REVERT: A 794 MET cc_start: 0.1084 (tpp) cc_final: 0.0686 (ptp) REVERT: A 809 MET cc_start: 0.5295 (mmp) cc_final: 0.4850 (mtt) REVERT: A 1260 MET cc_start: 0.1391 (OUTLIER) cc_final: 0.0508 (ppp) REVERT: A 1348 MET cc_start: 0.0101 (mmt) cc_final: -0.1271 (ttm) REVERT: A 1379 MET cc_start: 0.1951 (mmm) cc_final: 0.1164 (tmm) REVERT: B 269 MET cc_start: 0.2677 (tpt) cc_final: 0.1438 (ppp) REVERT: B 314 ARG cc_start: 0.3229 (OUTLIER) cc_final: 0.1665 (mtt180) REVERT: B 358 MET cc_start: 0.0024 (mmp) cc_final: -0.0557 (ptm) REVERT: B 360 MET cc_start: 0.2687 (mmt) cc_final: 0.2315 (mmp) REVERT: B 420 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.5200 (tp) REVERT: B 435 ARG cc_start: 0.7592 (mpt-90) cc_final: 0.7363 (mtt90) REVERT: B 496 MET cc_start: 0.3515 (tpt) cc_final: 0.3249 (mtt) REVERT: B 560 THR cc_start: 0.5654 (p) cc_final: 0.5306 (p) REVERT: B 586 GLU cc_start: 0.4807 (tm-30) cc_final: 0.2819 (tt0) REVERT: B 987 MET cc_start: 0.0036 (mmm) cc_final: -0.0207 (ptp) REVERT: C 71 MET cc_start: 0.8642 (tpp) cc_final: 0.7785 (mtt) REVERT: D 153 MET cc_start: 0.1499 (mmm) cc_final: 0.1100 (mmm) REVERT: E 1 MET cc_start: 0.1723 (tpt) cc_final: 0.0534 (ptm) REVERT: G 89 ILE cc_start: 0.3357 (OUTLIER) cc_final: 0.3013 (mt) REVERT: G 105 PHE cc_start: 0.2451 (OUTLIER) cc_final: 0.0182 (t80) REVERT: G 115 LEU cc_start: 0.0389 (OUTLIER) cc_final: -0.1045 (tp) REVERT: H 102 TYR cc_start: 0.2751 (p90) cc_final: 0.2323 (p90) REVERT: K 99 ASN cc_start: 0.8005 (p0) cc_final: 0.7757 (p0) REVERT: K 133 SER cc_start: 0.6224 (m) cc_final: 0.5866 (p) REVERT: K 142 MET cc_start: 0.3824 (mpp) cc_final: 0.1746 (mmt) REVERT: N 297 MET cc_start: -0.1323 (mmt) cc_final: -0.2820 (mtt) REVERT: N 380 MET cc_start: 0.3747 (mmt) cc_final: 0.2699 (ttt) REVERT: O 137 ILE cc_start: 0.7047 (pp) cc_final: 0.6728 (pt) REVERT: O 144 MET cc_start: 0.5700 (mmm) cc_final: 0.5499 (mmp) REVERT: O 268 LYS cc_start: 0.3081 (pttt) cc_final: 0.2230 (mmtt) REVERT: O 287 PHE cc_start: 0.4084 (p90) cc_final: 0.3455 (p90) REVERT: O 293 SER cc_start: 0.7521 (p) cc_final: 0.6898 (m) REVERT: O 527 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4296 (tt) REVERT: O 546 VAL cc_start: 0.5018 (OUTLIER) cc_final: 0.3836 (p) REVERT: O 577 MET cc_start: 0.8117 (tpp) cc_final: 0.7913 (ttp) REVERT: P 172 ILE cc_start: 0.5387 (tp) cc_final: 0.4884 (tp) REVERT: P 241 ARG cc_start: 0.4204 (tpt170) cc_final: 0.3719 (tpt90) REVERT: P 299 MET cc_start: 0.4653 (ppp) cc_final: 0.3666 (ptm) REVERT: Q 75 MET cc_start: 0.1536 (mmt) cc_final: 0.0704 (mmm) outliers start: 79 outliers final: 57 residues processed: 554 average time/residue: 0.1898 time to fit residues: 179.2517 Evaluate side-chains 508 residues out of total 4429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 443 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 488 HIS Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1429 LYS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 CYS Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 287 HIS Chi-restraints excluded: chain N residue 309 LEU Chi-restraints excluded: chain N residue 373 VAL Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 207 HIS Chi-restraints excluded: chain O residue 289 LYS Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 471 THR Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain O residue 546 VAL Chi-restraints excluded: chain O residue 597 GLN Chi-restraints excluded: chain P residue 181 ILE Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 264 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 22 optimal weight: 0.2980 chunk 387 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 238 optimal weight: 0.6980 chunk 248 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 460 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 HIS ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 558 ASN ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 232 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** O 43 ASN ** 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 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.250652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.234165 restraints weight = 72514.795| |-----------------------------------------------------------------------------| r_work (start): 0.4558 rms_B_bonded: 1.53 r_work: 0.4421 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4347 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4349 r_free = 0.4349 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4349 r_free = 0.4349 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 1.5533 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= 0.153 Angle : 0.813 24.881 56036 Z= 0.406 Chirality : 0.048 0.288 6312 Planarity : 0.006 0.073 7090 Dihedral : 10.889 83.389 5907 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.77 % Favored : 84.09 % Rotamer: Outliers : 1.80 % Allowed : 21.10 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.15 % Twisted Proline : 1.82 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.11), residues: 4965 helix: -1.03 (0.13), residues: 1522 sheet: -2.19 (0.25), residues: 417 loop : -3.25 (0.10), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 372 TYR 0.030 0.002 TYR B 762 PHE 0.028 0.002 PHE A 474 TRP 0.032 0.002 TRP B 442 HIS 0.011 0.001 HIS B 672 Details of bonding type rmsd covalent geometry : bond 0.00343 (41361) covalent geometry : angle 0.81326 (56036) hydrogen bonds : bond 0.03412 ( 908) hydrogen bonds : angle 5.05810 ( 2571) metal coordination : bond 0.00232 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8583.51 seconds wall clock time: 147 minutes 58.07 seconds (8878.07 seconds total)