Starting phenix.real_space_refine on Tue Sep 15 20:40:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gej_4395/09_2026/6gej_4395.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gej_4395/09_2026/6gej_4395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gej_4395/09_2026/6gej_4395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gej_4395/09_2026/6gej_4395.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6gej_4395/09_2026/6gej_4395.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gej_4395/09_2026/6gej_4395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gej_4395/09_2026/6gej_4395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gej_4395/09_2026/6gej_4395.map" } resolution = 3.6 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 966 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 324 5.49 5 Mg 8 5.21 5 S 118 5.16 5 Be 2 3.05 5 C 26529 2.51 5 N 7737 2.21 5 O 8976 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 174 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43702 Number of models: 1 Model: "" Number of chains: 29 Chain: "Z" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 655 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'TRANS': 130} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 131 Planarities with less than four sites: {'UNK:plan-1': 131} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 651 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3137 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "J" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3177 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "M" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5398 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 19, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 5, 'TRP:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 7, 'ASP:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 167 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1695 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 3 Chain: "T" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3391 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3299 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3336 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3325 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3410 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 436} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23040 SG CYS S 244 89.133 119.821 106.290 1.00 89.97 S ATOM 23060 SG CYS S 247 92.310 121.520 103.015 1.00 92.50 S ATOM 23176 SG CYS S 264 91.902 118.182 103.872 1.00 91.58 S ATOM 23201 SG CYS S 268 93.891 120.081 106.264 1.00102.36 S ATOM 23120 SG CYS S 256 87.365 114.091 115.274 1.00 92.66 S ATOM 23141 SG CYS S 259 85.271 117.144 116.015 1.00 90.81 S ATOM 23280 SG CYS S 277 87.907 117.396 119.028 1.00103.89 S Time building chain proxies: 8.82, per 1000 atoms: 0.20 Number of scatterers: 43702 At special positions: 0 Unit cell: (147.63, 197.58, 203.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 118 16.00 P 324 15.00 Mg 8 11.99 F 6 9.00 O 8976 8.00 N 7737 7.00 C 26529 6.00 Be 2 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 264 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " Number of angles added : 9 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9030 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 33 sheets defined 51.0% alpha, 11.0% beta 151 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'Z' and resid 101 through 129 Processing helix chain 'Z' and resid 136 through 144 removed outlier: 4.243A pdb=" N UNK Z 144 " --> pdb=" O UNK Z 140 " (cutoff:3.500A) Processing helix chain 'Z' and resid 198 through 200 No H-bonds generated for 'chain 'Z' and resid 198 through 200' Processing helix chain 'Z' and resid 201 through 207 Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.036A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.706A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 114 removed outlier: 3.546A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 44 through 56 removed outlier: 4.036A pdb=" N LEU B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 77 removed outlier: 3.707A pdb=" N PHE B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 114 removed outlier: 3.547A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.773A pdb=" N ILE C 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 49 through 76 removed outlier: 3.578A pdb=" N GLU C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.629A pdb=" N VAL C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 92 " --> pdb=" O TYR C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.773A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.578A pdb=" N GLU D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.628A pdb=" N VAL D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG D 92 " --> pdb=" O TYR D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 removed outlier: 4.305A pdb=" N LYS E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 22' Processing helix chain 'E' and resid 27 through 38 removed outlier: 3.791A pdb=" N VAL E 31 " --> pdb=" O PRO E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 74 removed outlier: 3.821A pdb=" N ASN E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 91 removed outlier: 3.566A pdb=" N LEU E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.532A pdb=" N ALA F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 18 through 22' Processing helix chain 'F' and resid 27 through 38 removed outlier: 3.792A pdb=" N VAL F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 74 removed outlier: 3.821A pdb=" N ASN F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.566A pdb=" N LEU F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 98 Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 58 through 87 removed outlier: 3.511A pdb=" N GLU G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 106 through 126 Processing helix chain 'H' and resid 40 through 52 Processing helix chain 'H' and resid 58 through 87 removed outlier: 3.510A pdb=" N GLU H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 106 through 125 Processing helix chain 'M' and resid 697 through 712 removed outlier: 4.163A pdb=" N SER M 709 " --> pdb=" O ASN M 705 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU M 710 " --> pdb=" O TRP M 706 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR M 711 " --> pdb=" O LEU M 707 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN M 712 " --> pdb=" O ALA M 708 " (cutoff:3.500A) Processing helix chain 'M' and resid 726 through 742 removed outlier: 3.532A pdb=" N GLN M 730 " --> pdb=" O GLY M 726 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA M 739 " --> pdb=" O LEU M 735 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS M 740 " --> pdb=" O ALA M 736 " (cutoff:3.500A) Processing helix chain 'M' and resid 756 through 767 removed outlier: 3.919A pdb=" N GLU M 761 " --> pdb=" O LEU M 757 " (cutoff:3.500A) Processing helix chain 'M' and resid 781 through 787 Processing helix chain 'M' and resid 804 through 809 removed outlier: 4.016A pdb=" N GLN M 808 " --> pdb=" O GLN M 804 " (cutoff:3.500A) Processing helix chain 'M' and resid 809 through 814 Processing helix chain 'M' and resid 834 through 842 removed outlier: 4.092A pdb=" N GLN M 838 " --> pdb=" O SER M 834 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU M 841 " --> pdb=" O TRP M 837 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN M 842 " --> pdb=" O GLN M 838 " (cutoff:3.500A) Processing helix chain 'M' and resid 859 through 871 removed outlier: 3.922A pdb=" N LEU M 863 " --> pdb=" O ASN M 859 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET M 871 " --> pdb=" O LEU M 867 " (cutoff:3.500A) Processing helix chain 'M' and resid 914 through 925 removed outlier: 3.687A pdb=" N HIS M 922 " --> pdb=" O VAL M 918 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN M 923 " --> pdb=" O ALA M 919 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL M 924 " --> pdb=" O LYS M 920 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU M 925 " --> pdb=" O LEU M 921 " (cutoff:3.500A) Processing helix chain 'M' and resid 954 through 971 Processing helix chain 'M' and resid 972 through 975 removed outlier: 3.944A pdb=" N ALA M 975 " --> pdb=" O ALA M 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 972 through 975' Processing helix chain 'M' and resid 978 through 994 removed outlier: 3.898A pdb=" N ILE M 982 " --> pdb=" O ASN M 978 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL M 983 " --> pdb=" O PHE M 979 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN M 988 " --> pdb=" O ASN M 984 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU M 989 " --> pdb=" O CYS M 985 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASN M 994 " --> pdb=" O ARG M 990 " (cutoff:3.500A) Processing helix chain 'M' and resid 1013 through 1030 removed outlier: 3.850A pdb=" N ASP M1017 " --> pdb=" O CYS M1013 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR M1018 " --> pdb=" O VAL M1014 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP M1020 " --> pdb=" O SER M1016 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL M1021 " --> pdb=" O ASP M1017 " (cutoff:3.500A) Processing helix chain 'M' and resid 1046 through 1050 Processing helix chain 'M' and resid 1056 through 1065 Processing helix chain 'M' and resid 1069 through 1094 removed outlier: 3.585A pdb=" N LEU M1078 " --> pdb=" O GLU M1074 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU M1080 " --> pdb=" O ASN M1076 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU M1085 " --> pdb=" O THR M1081 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU M1088 " --> pdb=" O GLN M1084 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU M1091 " --> pdb=" O GLU M1087 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ALA M1092 " --> pdb=" O GLU M1088 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE M1094 " --> pdb=" O GLY M1090 " (cutoff:3.500A) Processing helix chain 'M' and resid 1103 through 1133 removed outlier: 4.513A pdb=" N SER M1107 " --> pdb=" O TYR M1103 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN M1108 " --> pdb=" O PHE M1104 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP M1117 " --> pdb=" O GLU M1113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET M1118 " --> pdb=" O GLY M1114 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU M1122 " --> pdb=" O MET M1118 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS M1123 " --> pdb=" O LEU M1119 " (cutoff:3.500A) Processing helix chain 'M' and resid 1141 through 1147 Processing helix chain 'M' and resid 1159 through 1164 removed outlier: 3.994A pdb=" N LYS M1164 " --> pdb=" O ASN M1160 " (cutoff:3.500A) Processing helix chain 'M' and resid 1165 through 1173 removed outlier: 3.800A pdb=" N LEU M1171 " --> pdb=" O GLN M1167 " (cutoff:3.500A) Processing helix chain 'M' and resid 1173 through 1181 Processing helix chain 'M' and resid 1191 through 1198 removed outlier: 3.901A pdb=" N LEU M1195 " --> pdb=" O ASP M1191 " (cutoff:3.500A) Processing helix chain 'M' and resid 1206 through 1220 removed outlier: 3.592A pdb=" N ARG M1210 " --> pdb=" O GLY M1206 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU M1211 " --> pdb=" O GLU M1207 " (cutoff:3.500A) Processing helix chain 'M' and resid 1224 through 1233 removed outlier: 3.573A pdb=" N ILE M1233 " --> pdb=" O THR M1229 " (cutoff:3.500A) Processing helix chain 'M' and resid 1239 through 1244 removed outlier: 4.171A pdb=" N TYR M1243 " --> pdb=" O SER M1239 " (cutoff:3.500A) Processing helix chain 'M' and resid 1250 through 1261 Processing helix chain 'M' and resid 1272 through 1286 removed outlier: 3.917A pdb=" N ASP M1276 " --> pdb=" O THR M1272 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL M1277 " --> pdb=" O LYS M1273 " (cutoff:3.500A) Processing helix chain 'M' and resid 1298 through 1310 removed outlier: 4.058A pdb=" N GLN M1302 " --> pdb=" O ILE M1298 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE M1303 " --> pdb=" O GLU M1299 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE M1308 " --> pdb=" O LEU M1304 " (cutoff:3.500A) Processing helix chain 'M' and resid 1348 through 1356 removed outlier: 3.745A pdb=" N GLN M1352 " --> pdb=" O ASP M1348 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS M1355 " --> pdb=" O CYS M1351 " (cutoff:3.500A) Processing helix chain 'M' and resid 1374 through 1386 removed outlier: 3.656A pdb=" N LEU M1380 " --> pdb=" O GLU M1376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS M1381 " --> pdb=" O SER M1377 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN M1385 " --> pdb=" O LYS M1381 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 49 removed outlier: 4.068A pdb=" N LYS R 47 " --> pdb=" O ASN R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 82 removed outlier: 4.002A pdb=" N GLU R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 132 through 137 removed outlier: 4.000A pdb=" N PHE R 136 " --> pdb=" O PRO R 132 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 132 through 137' Processing helix chain 'R' and resid 138 through 143 removed outlier: 4.049A pdb=" N LYS R 141 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR R 143 " --> pdb=" O THR R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 235 Processing helix chain 'R' and resid 241 through 253 removed outlier: 4.012A pdb=" N VAL R 245 " --> pdb=" O GLU R 241 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU R 253 " --> pdb=" O LYS R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 266 Processing helix chain 'R' and resid 307 through 313 removed outlier: 4.355A pdb=" N PHE R 311 " --> pdb=" O THR R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 317 Processing helix chain 'R' and resid 319 through 324 removed outlier: 3.760A pdb=" N ILE R 322 " --> pdb=" O HIS R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 340 Processing helix chain 'R' and resid 345 through 350 Processing helix chain 'R' and resid 358 through 362 removed outlier: 3.696A pdb=" N LEU R 362 " --> pdb=" O ASN R 359 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 377 removed outlier: 3.854A pdb=" N GLN R 376 " --> pdb=" O GLU R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 406 removed outlier: 3.896A pdb=" N ALA R 404 " --> pdb=" O MET R 400 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 413 removed outlier: 3.995A pdb=" N LYS R 411 " --> pdb=" O ASP R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 415 through 422 Processing helix chain 'R' and resid 423 through 430 removed outlier: 3.844A pdb=" N CYS R 427 " --> pdb=" O GLY R 423 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 61 Processing helix chain 'S' and resid 91 through 107 Processing helix chain 'S' and resid 115 through 125 removed outlier: 3.749A pdb=" N LEU S 119 " --> pdb=" O ASN S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 135 removed outlier: 3.509A pdb=" N ILE S 131 " --> pdb=" O PRO S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 179 Processing helix chain 'S' and resid 180 through 182 No H-bonds generated for 'chain 'S' and resid 180 through 182' Processing helix chain 'S' and resid 192 through 203 Processing helix chain 'S' and resid 207 through 214 Processing helix chain 'S' and resid 218 through 226 Processing helix chain 'S' and resid 265 through 273 Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.522A pdb=" N VAL T 60 " --> pdb=" O GLU T 56 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE T 61 " --> pdb=" O ALA T 57 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 removed outlier: 3.781A pdb=" N SER T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 110 No H-bonds generated for 'chain 'T' and resid 108 through 110' Processing helix chain 'T' and resid 116 through 129 removed outlier: 3.510A pdb=" N THR T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE T 129 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 193 Processing helix chain 'T' and resid 217 through 222 removed outlier: 3.994A pdb=" N THR T 220 " --> pdb=" O ALA T 217 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE T 222 " --> pdb=" O ALA T 219 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 258 Processing helix chain 'T' and resid 264 through 273 Processing helix chain 'T' and resid 281 through 296 removed outlier: 3.653A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 313 through 316 Processing helix chain 'T' and resid 317 through 329 removed outlier: 3.640A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU T 329 " --> pdb=" O ASN T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 359 Processing helix chain 'T' and resid 360 through 367 removed outlier: 3.724A pdb=" N ARG T 366 " --> pdb=" O ASP T 362 " (cutoff:3.500A) Processing helix chain 'T' and resid 376 through 392 Processing helix chain 'T' and resid 396 through 410 removed outlier: 3.602A pdb=" N LEU T 402 " --> pdb=" O SER T 398 " (cutoff:3.500A) Processing helix chain 'T' and resid 411 through 429 removed outlier: 3.890A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix removed outlier: 4.192A pdb=" N ILE T 424 " --> pdb=" O ALA T 420 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 removed outlier: 3.974A pdb=" N LEU T 444 " --> pdb=" O ASN T 440 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU T 445 " --> pdb=" O GLU T 441 " (cutoff:3.500A) Processing helix chain 'T' and resid 448 through 458 removed outlier: 3.886A pdb=" N THR T 458 " --> pdb=" O LYS T 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 81 through 93 removed outlier: 3.651A pdb=" N ALA U 85 " --> pdb=" O LYS U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 124 removed outlier: 3.800A pdb=" N ALA U 120 " --> pdb=" O ALA U 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE U 121 " --> pdb=" O LEU U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 182 removed outlier: 3.519A pdb=" N GLU U 182 " --> pdb=" O GLY U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 250 removed outlier: 3.694A pdb=" N ILE U 247 " --> pdb=" O GLU U 243 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN U 248 " --> pdb=" O ILE U 244 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER U 249 " --> pdb=" O ASP U 245 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 260 removed outlier: 3.556A pdb=" N PHE U 258 " --> pdb=" O PHE U 254 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 283 removed outlier: 3.726A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR U 275 " --> pdb=" O ASP U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 301 Processing helix chain 'U' and resid 302 through 314 removed outlier: 3.618A pdb=" N ASN U 310 " --> pdb=" O PHE U 306 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 343 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.823A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 375 removed outlier: 3.694A pdb=" N LYS U 365 " --> pdb=" O GLU U 361 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR U 366 " --> pdb=" O GLN U 362 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.769A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG U 413 " --> pdb=" O ILE U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.520A pdb=" N PHE U 430 " --> pdb=" O ALA U 426 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 444 removed outlier: 3.642A pdb=" N GLU U 442 " --> pdb=" O LYS U 438 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 68 Processing helix chain 'V' and resid 84 through 97 removed outlier: 3.591A pdb=" N ALA V 91 " --> pdb=" O ALA V 87 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER V 93 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY V 97 " --> pdb=" O SER V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.787A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 128 removed outlier: 3.742A pdb=" N ASN V 124 " --> pdb=" O THR V 120 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE V 125 " --> pdb=" O LEU V 121 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG V 126 " --> pdb=" O MET V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 182 through 192 Processing helix chain 'V' and resid 217 through 219 No H-bonds generated for 'chain 'V' and resid 217 through 219' Processing helix chain 'V' and resid 249 through 258 removed outlier: 3.581A pdb=" N ALA V 255 " --> pdb=" O ASP V 251 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN V 256 " --> pdb=" O LEU V 252 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 274 removed outlier: 4.283A pdb=" N LYS V 274 " --> pdb=" O GLY V 270 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.509A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN V 298 " --> pdb=" O LYS V 294 " (cutoff:3.500A) Processing helix chain 'V' and resid 313 through 316 Processing helix chain 'V' and resid 317 through 328 removed outlier: 3.738A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 366 removed outlier: 3.690A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 418 removed outlier: 3.691A pdb=" N ALA V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 429 Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.517A pdb=" N ILE W 57 " --> pdb=" O ALA W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 93 removed outlier: 3.884A pdb=" N GLY W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 125 removed outlier: 3.974A pdb=" N SER W 124 " --> pdb=" O ALA W 120 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE W 125 " --> pdb=" O PHE W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 182 removed outlier: 3.862A pdb=" N ASP W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 248 removed outlier: 3.573A pdb=" N ASN W 248 " --> pdb=" O ILE W 244 " (cutoff:3.500A) Processing helix chain 'W' and resid 251 through 253 No H-bonds generated for 'chain 'W' and resid 251 through 253' Processing helix chain 'W' and resid 254 through 260 removed outlier: 4.319A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.507A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR W 275 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.872A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 343 removed outlier: 3.534A pdb=" N LEU W 343 " --> pdb=" O PRO W 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 340 through 343' Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.992A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 376 removed outlier: 3.508A pdb=" N LYS W 365 " --> pdb=" O GLU W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 412 removed outlier: 3.571A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN W 407 " --> pdb=" O ILE W 403 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN W 408 " --> pdb=" O SER W 404 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS W 412 " --> pdb=" O GLN W 408 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 Processing helix chain 'W' and resid 432 through 443 removed outlier: 3.712A pdb=" N LYS W 438 " --> pdb=" O ALA W 434 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR W 439 " --> pdb=" O ARG W 435 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.912A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 removed outlier: 3.667A pdb=" N LEU X 88 " --> pdb=" O GLY X 84 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA X 89 " --> pdb=" O LYS X 85 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY X 97 " --> pdb=" O SER X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.706A pdb=" N TYR X 111 " --> pdb=" O SER X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 108 through 111' Processing helix chain 'X' and resid 116 through 127 Processing helix chain 'X' and resid 184 through 193 removed outlier: 4.332A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 219 No H-bonds generated for 'chain 'X' and resid 217 through 219' Processing helix chain 'X' and resid 249 through 258 removed outlier: 3.582A pdb=" N ALA X 255 " --> pdb=" O ASP X 251 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 271 Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.545A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN X 298 " --> pdb=" O LYS X 294 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 316 Processing helix chain 'X' and resid 317 through 328 removed outlier: 3.575A pdb=" N ASN X 325 " --> pdb=" O PHE X 321 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 359 Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 392 removed outlier: 3.848A pdb=" N THR X 389 " --> pdb=" O GLU X 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL X 390 " --> pdb=" O ARG X 386 " (cutoff:3.500A) Processing helix chain 'X' and resid 397 through 410 removed outlier: 3.686A pdb=" N LEU X 402 " --> pdb=" O SER X 398 " (cutoff:3.500A) Processing helix chain 'X' and resid 411 through 418 removed outlier: 3.771A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 429 Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 removed outlier: 3.772A pdb=" N GLU X 457 " --> pdb=" O THR X 453 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR X 458 " --> pdb=" O LYS X 454 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 64 removed outlier: 3.674A pdb=" N ILE Y 57 " --> pdb=" O ALA Y 53 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 81 through 93 removed outlier: 3.536A pdb=" N ALA Y 85 " --> pdb=" O LYS Y 81 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 removed outlier: 3.996A pdb=" N LYS Y 181 " --> pdb=" O ASP Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 209 Processing helix chain 'Y' and resid 241 through 250 removed outlier: 3.580A pdb=" N ARG Y 250 " --> pdb=" O VAL Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 260 Processing helix chain 'Y' and resid 266 through 283 removed outlier: 4.087A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP Y 271 " --> pdb=" O SER Y 267 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN Y 272 " --> pdb=" O GLU Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 313 Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 Processing helix chain 'Y' and resid 360 through 376 removed outlier: 3.519A pdb=" N LYS Y 365 " --> pdb=" O GLU Y 361 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR Y 366 " --> pdb=" O GLN Y 362 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU Y 374 " --> pdb=" O ILE Y 370 " (cutoff:3.500A) Processing helix chain 'Y' and resid 382 through 394 removed outlier: 3.621A pdb=" N LEU Y 386 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU Y 393 " --> pdb=" O LYS Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.793A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER Y 400 " --> pdb=" O LEU Y 396 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN Y 401 " --> pdb=" O ARG Y 397 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU Y 402 " --> pdb=" O TYR Y 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN Y 407 " --> pdb=" O ILE Y 403 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 Processing helix chain 'Y' and resid 432 through 443 removed outlier: 3.757A pdb=" N VAL Y 437 " --> pdb=" O SER Y 433 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'Z' and resid 169 through 171 Processing sheet with id=B, first strand: chain 'M' and resid 719 through 721 removed outlier: 5.480A pdb=" N LEU M 930 " --> pdb=" O ALA M 720 " (cutoff:3.500A) No H-bonds generated for sheet with id=B Processing sheet with id=C, first strand: chain 'M' and resid 800 through 802 removed outlier: 5.882A pdb=" N ILE M 750 " --> pdb=" O VAL M 801 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ARG M 847 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU M 823 " --> pdb=" O ARG M 847 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU M 849 " --> pdb=" O LEU M 823 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'M' and resid 944 through 946 removed outlier: 6.738A pdb=" N VAL M1364 " --> pdb=" O TYR M 945 " (cutoff:3.500A) No H-bonds generated for sheet with id=D Processing sheet with id=E, first strand: chain 'M' and resid 949 through 951 Processing sheet with id=F, first strand: chain 'M' and resid 1335 through 1338 removed outlier: 4.077A pdb=" N THR M1269 " --> pdb=" O LEU M1319 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET M1290 " --> pdb=" O VAL M1316 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'R' and resid 127 through 130 removed outlier: 6.397A pdb=" N ILE R 6 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER R 102 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE R 8 " --> pdb=" O SER R 102 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'R' and resid 32 through 35 Processing sheet with id=I, first strand: chain 'R' and resid 147 through 151 Processing sheet with id=J, first strand: chain 'R' and resid 353 through 356 removed outlier: 6.431A pdb=" N LEU R 189 " --> pdb=" O VAL R 354 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR R 356 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE R 191 " --> pdb=" O THR R 356 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'R' and resid 286 through 289 removed outlier: 3.976A pdb=" N TYR R 286 " --> pdb=" O VAL R 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL R 275 " --> pdb=" O TYR R 286 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'T' and resid 369 through 372 removed outlier: 8.558A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLY T 79 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER T 340 " --> pdb=" O GLY T 79 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA T 339 " --> pdb=" O ILE T 310 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'T' and resid 246 through 248 Processing sheet with id=N, first strand: chain 'T' and resid 238 through 243 removed outlier: 3.713A pdb=" N GLY T 213 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'T' and resid 147 through 150 removed outlier: 3.593A pdb=" N HIS T 165 " --> pdb=" O GLU T 150 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'U' and resid 351 through 355 removed outlier: 7.208A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA U 324 " --> pdb=" O ILE U 295 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'U' and resid 286 through 290 removed outlier: 3.605A pdb=" N GLY U 126 " --> pdb=" O VAL U 289 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'U' and resid 166 through 170 removed outlier: 3.567A pdb=" N THR U 167 " --> pdb=" O ILE U 160 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU U 142 " --> pdb=" O THR U 159 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL U 140 " --> pdb=" O ASP U 188 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'V' and resid 367 through 371 removed outlier: 7.130A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'V' and resid 246 through 248 removed outlier: 3.536A pdb=" N LEU V 131 " --> pdb=" O VAL V 247 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG V 132 " --> pdb=" O GLU V 302 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'V' and resid 238 through 243 removed outlier: 3.740A pdb=" N LYS V 241 " --> pdb=" O LYS V 137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY V 142 " --> pdb=" O ILE V 200 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE V 200 " --> pdb=" O GLY V 142 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'V' and resid 147 through 149 removed outlier: 3.825A pdb=" N THR V 148 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE V 167 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=X, first strand: chain 'W' and resid 351 through 354 removed outlier: 7.304A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'W' and resid 230 through 240 Processing sheet with id=Z, first strand: chain 'W' and resid 166 through 171 removed outlier: 4.273A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE W 190 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL W 140 " --> pdb=" O ASP W 188 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL W 189 " --> pdb=" O GLY W 203 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'X' and resid 367 through 371 removed outlier: 7.568A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA X 339 " --> pdb=" O ILE X 310 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'X' and resid 238 through 248 removed outlier: 3.706A pdb=" N LYS X 241 " --> pdb=" O LYS X 137 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'X' and resid 139 through 142 removed outlier: 3.912A pdb=" N GLY X 142 " --> pdb=" O ILE X 200 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY X 213 " --> pdb=" O VAL X 199 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'X' and resid 175 through 182 removed outlier: 7.010A pdb=" N GLU X 150 " --> pdb=" O SER X 164 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL X 166 " --> pdb=" O THR X 148 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR X 148 " --> pdb=" O VAL X 166 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'Y' and resid 353 through 355 removed outlier: 8.530A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL Y 321 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL Y 73 " --> pdb=" O VAL Y 321 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N MET Y 323 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA Y 324 " --> pdb=" O ILE Y 295 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'Y' and resid 230 through 240 removed outlier: 3.625A pdb=" N LEU Y 135 " --> pdb=" O LYS Y 231 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'Y' and resid 166 through 170 removed outlier: 3.844A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP Y 188 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) 1616 hydrogen bonds defined for protein. 4725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 12.49 Time building geometry restraints manager: 4.16 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: 12690 1.34 - 1.46: 7653 1.46 - 1.57: 23823 1.57 - 1.69: 638 1.69 - 1.81: 194 Bond restraints: 44998 Sorted by residual: bond pdb=" F2 BEF R 502 " pdb="BE BEF R 502 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" F2 BEF M1602 " pdb="BE BEF M1602 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F3 BEF M1602 " pdb="BE BEF M1602 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" F3 BEF R 502 " pdb="BE BEF R 502 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C3' DC I -29 " pdb=" C2' DC I -29 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 ... (remaining 44993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 61617 2.56 - 5.12: 528 5.12 - 7.68: 55 7.68 - 10.25: 2 10.25 - 12.81: 5 Bond angle restraints: 62207 Sorted by residual: angle pdb=" O4' DG I 48 " pdb=" C4' DG I 48 " pdb=" C3' DG I 48 " ideal model delta sigma weight residual 106.00 101.72 4.28 6.00e-01 2.78e+00 5.10e+01 angle pdb=" C LEU M 998 " pdb=" N PHE M 999 " pdb=" CA PHE M 999 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.39e+01 angle pdb=" N MET V 406 " pdb=" CA MET V 406 " pdb=" C MET V 406 " ideal model delta sigma weight residual 110.97 105.70 5.27 1.09e+00 8.42e-01 2.34e+01 angle pdb=" C LEU U 29 " pdb=" CA LEU U 29 " pdb=" CB LEU U 29 " ideal model delta sigma weight residual 116.54 111.05 5.49 1.15e+00 7.56e-01 2.28e+01 angle pdb=" N3 DT J -65 " pdb=" C4 DT J -65 " pdb=" O4 DT J -65 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 62202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 24967 35.89 - 71.79: 1595 71.79 - 107.68: 34 107.68 - 143.57: 9 143.57 - 179.46: 4 Dihedral angle restraints: 26609 sinusoidal: 12658 harmonic: 13951 Sorted by residual: dihedral pdb=" CA UNK Z 188 " pdb=" C UNK Z 188 " pdb=" N UNK Z 189 " pdb=" CA UNK Z 189 " ideal model delta harmonic sigma weight residual -180.00 -139.72 -40.28 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA LEU M 692 " pdb=" C LEU M 692 " pdb=" N ARG M 693 " pdb=" CA ARG M 693 " ideal model delta harmonic sigma weight residual 180.00 -143.52 -36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" C5' ADP W 501 " pdb=" O5' ADP W 501 " pdb=" PA ADP W 501 " pdb=" O2A ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 119.47 -179.46 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 26606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 5064 0.035 - 0.069: 1548 0.069 - 0.104: 502 0.104 - 0.139: 170 0.139 - 0.173: 4 Chirality restraints: 7288 Sorted by residual: chirality pdb=" CA MET V 406 " pdb=" N MET V 406 " pdb=" C MET V 406 " pdb=" CB MET V 406 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA TYR V 462 " pdb=" N TYR V 462 " pdb=" C TYR V 462 " pdb=" CB TYR V 462 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 7285 not shown) Planarity restraints: 6836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE T 304 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO T 305 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO T 305 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO T 305 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 998 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C LEU M 998 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU M 998 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE M 999 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP V 182 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO V 183 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO V 183 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO V 183 " 0.027 5.00e-02 4.00e+02 ... (remaining 6833 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 10 2.17 - 2.85: 14039 2.85 - 3.54: 60125 3.54 - 4.22: 103118 4.22 - 4.90: 168232 Nonbonded interactions: 345524 Sorted by model distance: nonbonded pdb=" CE MET T 406 " pdb=" CD1 LEU T 418 " model vdw 1.491 3.880 nonbonded pdb=" OG1 THR Y 82 " pdb="MG MG Y 502 " model vdw 2.076 2.170 nonbonded pdb=" O1B ADP R 501 " pdb="MG MG R 503 " model vdw 2.077 2.170 nonbonded pdb=" N2 DG I -68 " pdb=" O2 DC J 68 " model vdw 2.132 2.496 nonbonded pdb=" OG1 THR U 162 " pdb=" O MET U 165 " model vdw 2.140 3.040 ... (remaining 345519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 23 through 102) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 17 through 117) selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 35 through 125) selection = chain 'H' } ncs_group { reference = (chain 'T' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 501)) selection = (chain 'V' and (resid 22 through 161 or (resid 162 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 501)) selection = (chain 'X' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 161 through 163 and (name N or name CA or \ name C or name O or name CB )) or resid 164 through 501)) } ncs_group { reference = (chain 'U' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 222 or (resid 223 and (name N or name C \ A or name C or name O or name CB )) or resid 224 through 459)) selection = (chain 'W' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 205 or resid 222 throug \ h 459)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 205 or resid 222 or (resid 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 through 45 \ 9)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.050 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 49.520 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.008 0.900 45008 Z= 0.682 Angle : 0.722 33.315 62216 Z= 0.493 Chirality : 0.040 0.173 7288 Planarity : 0.003 0.056 6836 Dihedral : 18.743 179.465 17579 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 3.93 % Allowed : 7.97 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.10), residues: 4633 helix: -2.29 (0.08), residues: 2159 sheet: -0.39 (0.18), residues: 655 loop : -1.42 (0.12), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M1133 TYR 0.016 0.001 TYR V 462 PHE 0.011 0.001 PHE Y 221 TRP 0.010 0.001 TRP M 790 HIS 0.009 0.001 HIS W 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.30 (44998) covalent geometry : angle 0.67848 / 0.49 (62207) hydrogen bonds : bond 0.16827 / 10.76 ( 1999) hydrogen bonds : angle 7.96102 / 5.35 ( 5463) metal coordination : bond 0.30947 / 15.79 ( 8) metal coordination : angle 20.55390 / 10.19 ( 9) Misc. bond : bond 0.89958 / 45.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 966 time to evaluate : 1.137 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 46 VAL cc_start: 0.8302 (t) cc_final: 0.7982 (t) REVERT: A 56 LYS cc_start: 0.7125 (mttm) cc_final: 0.6476 (tttm) REVERT: A 78 PHE cc_start: 0.4966 (m-10) cc_final: 0.4195 (m-80) REVERT: A 83 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7498 (ttt180) REVERT: B 68 GLN cc_start: 0.7907 (tp40) cc_final: 0.7574 (tt0) REVERT: C 58 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8331 (tp) REVERT: C 59 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7974 (tttp) REVERT: C 71 THR cc_start: 0.8378 (m) cc_final: 0.8003 (p) REVERT: C 91 LYS cc_start: 0.9007 (tppt) cc_final: 0.8524 (pptt) REVERT: D 35 ARG cc_start: 0.6704 (ttm-80) cc_final: 0.6490 (ttm110) REVERT: D 53 GLU cc_start: 0.7633 (tp30) cc_final: 0.6729 (mm-30) REVERT: D 64 SER cc_start: 0.9006 (m) cc_final: 0.8752 (t) REVERT: D 92 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6616 (mtp-110) REVERT: E 58 TYR cc_start: 0.7268 (t80) cc_final: 0.7029 (t80) REVERT: E 82 ARG cc_start: 0.7948 (ttt-90) cc_final: 0.7651 (ttt90) REVERT: F 26 PHE cc_start: 0.7298 (m-80) cc_final: 0.6730 (m-80) REVERT: F 30 ARG cc_start: 0.4050 (mmt90) cc_final: 0.3831 (mpt180) REVERT: F 36 ARG cc_start: 0.6370 (ttm110) cc_final: 0.6108 (mmm-85) REVERT: F 102 THR cc_start: 0.9021 (m) cc_final: 0.8714 (p) REVERT: G 74 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7696 (tm-30) REVERT: G 89 LYS cc_start: 0.5891 (mttt) cc_final: 0.5345 (ptmt) REVERT: G 109 LEU cc_start: 0.8783 (mt) cc_final: 0.8326 (mm) REVERT: H 46 LYS cc_start: 0.7145 (mttt) cc_final: 0.6857 (ttmm) REVERT: H 70 ASN cc_start: 0.7407 (t0) cc_final: 0.6816 (t0) REVERT: M 848 ARG cc_start: 0.6693 (mtt90) cc_final: 0.6119 (mtt90) REVERT: M 980 MET cc_start: 0.7364 (mmt) cc_final: 0.6268 (ptp) REVERT: M 1082 ASN cc_start: 0.5809 (OUTLIER) cc_final: 0.5593 (m-40) REVERT: M 1199 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9055 (pp) REVERT: R 3 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7693 (p) REVERT: R 66 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6783 (pt) REVERT: R 70 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: R 190 VAL cc_start: 0.8775 (t) cc_final: 0.8483 (m) REVERT: R 199 TRP cc_start: 0.7195 (m100) cc_final: 0.6739 (m100) REVERT: R 331 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7950 (t) REVERT: R 345 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7644 (m) REVERT: S 202 LEU cc_start: 0.3756 (mt) cc_final: 0.3452 (mm) REVERT: S 220 MET cc_start: 0.7013 (ttp) cc_final: 0.5952 (tpt) REVERT: T 375 TYR cc_start: 0.6578 (m-80) cc_final: 0.6079 (m-80) REVERT: U 81 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6948 (ttpt) REVERT: U 158 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9064 (pt) REVERT: V 342 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7758 (mtt90) REVERT: V 344 MET cc_start: 0.9293 (mmm) cc_final: 0.9091 (mmm) REVERT: V 365 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: W 149 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7000 (tp) REVERT: W 164 ASP cc_start: 0.7080 (m-30) cc_final: 0.6379 (p0) REVERT: W 175 MET cc_start: 0.8714 (mmm) cc_final: 0.8497 (tpp) REVERT: W 323 MET cc_start: 0.7919 (mtt) cc_final: 0.7711 (mtt) REVERT: X 85 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8301 (mtmm) REVERT: X 210 LYS cc_start: 0.8120 (tttt) cc_final: 0.7875 (tppt) REVERT: X 312 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: Y 23 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7870 (p90) REVERT: Y 310 ASN cc_start: 0.7707 (m-40) cc_final: 0.7401 (m110) outliers start: 157 outliers final: 35 residues processed: 1091 average time/residue: 0.2787 time to fit residues: 481.3527 Evaluate side-chains 463 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 411 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1199 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain T residue 256 ASN Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain V residue 342 ARG Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 365 ASP Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 0.0040 chunk 215 optimal weight: 0.0270 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 42 GLN E 74 ASN E 115 ASN F 39 ASN F 115 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS M 716 ASN M 759 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 857 GLN M 940 GLN M1058 HIS M1226 GLN M1249 GLN M1302 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 HIS ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 GLN R 374 GLN S 176 GLN T 256 ASN T 271 GLN U 119 GLN U 155 GLN U 252 GLN U 451 GLN V 27 HIS V 124 ASN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 357 HIS W 455 GLN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 238 HIS X 256 ASN X 271 GLN X 417 GLN Y 23 HIS Y 36 GLN Y 144 GLN Y 223 GLN Y 272 GLN Y 443 ASN Y 451 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.123608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094312 restraints weight = 112254.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093565 restraints weight = 85364.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.093920 restraints weight = 63063.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094126 restraints weight = 54346.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094236 restraints weight = 50120.960| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 45008 Z= 0.195 Angle : 0.713 13.558 62216 Z= 0.372 Chirality : 0.045 0.249 7288 Planarity : 0.005 0.079 6836 Dihedral : 23.257 160.349 8728 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.13 % Favored : 96.85 % Rotamer: Outliers : 4.18 % Allowed : 14.23 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.11), residues: 4633 helix: -0.75 (0.10), residues: 2203 sheet: 0.01 (0.18), residues: 685 loop : -1.37 (0.13), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 967 TYR 0.019 0.002 TYR G 86 PHE 0.023 0.002 PHE R 120 TRP 0.015 0.002 TRP R 199 HIS 0.009 0.001 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (44998) covalent geometry : angle 0.70808 / 0.37 (62207) hydrogen bonds : bond 0.05975 / 3.67 ( 1999) hydrogen bonds : angle 5.26706 / 3.58 ( 5463) metal coordination : bond 0.01754 / 1.03 ( 8) metal coordination : angle 7.09304 / 3.62 ( 9) Misc. bond : bond 0.00540 / 0.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 419 time to evaluate : 1.810 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: A 56 LYS cc_start: 0.7333 (mttm) cc_final: 0.6365 (tttm) REVERT: C 62 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8176 (mm) REVERT: C 68 ASP cc_start: 0.8306 (m-30) cc_final: 0.8075 (m-30) REVERT: C 71 THR cc_start: 0.8880 (m) cc_final: 0.8339 (p) REVERT: C 77 LYS cc_start: 0.8553 (mmmm) cc_final: 0.7761 (mptt) REVERT: D 53 GLU cc_start: 0.7302 (tp30) cc_final: 0.6942 (mm-30) REVERT: D 92 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7211 (ptm160) REVERT: G 89 LYS cc_start: 0.6532 (mttt) cc_final: 0.5917 (ptmm) REVERT: G 103 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7348 (pp) REVERT: H 62 MET cc_start: 0.5852 (tmm) cc_final: 0.5643 (ttt) REVERT: H 111 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7589 (ptmm) REVERT: M 848 ARG cc_start: 0.6461 (mtt90) cc_final: 0.5706 (mtt90) REVERT: M 980 MET cc_start: 0.7377 (mmt) cc_final: 0.6550 (ptp) REVERT: M 987 MET cc_start: 0.7620 (tpp) cc_final: 0.7343 (tpp) REVERT: M 1082 ASN cc_start: 0.5986 (OUTLIER) cc_final: 0.5713 (m-40) REVERT: R 3 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7610 (p) REVERT: R 429 LYS cc_start: 0.7307 (tttt) cc_final: 0.6829 (mmmt) REVERT: S 7 GLU cc_start: 0.7977 (tp30) cc_final: 0.7458 (tp30) REVERT: S 179 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.6125 (p90) REVERT: S 220 MET cc_start: 0.6925 (ttp) cc_final: 0.5970 (tpt) REVERT: U 81 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7899 (ttmm) REVERT: U 226 GLU cc_start: 0.6771 (pm20) cc_final: 0.6557 (pm20) REVERT: U 300 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7218 (mtp) REVERT: U 301 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8261 (mp) REVERT: V 70 MET cc_start: 0.7059 (mmm) cc_final: 0.6714 (mmm) REVERT: W 164 ASP cc_start: 0.7240 (m-30) cc_final: 0.6400 (p0) REVERT: W 175 MET cc_start: 0.8571 (mmm) cc_final: 0.8277 (tpp) REVERT: X 312 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: Y 210 ARG cc_start: 0.7570 (mmm160) cc_final: 0.7349 (mmm160) REVERT: Y 310 ASN cc_start: 0.7806 (m-40) cc_final: 0.7536 (m110) REVERT: Y 325 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.9075 (t) REVERT: Y 443 ASN cc_start: 0.7114 (OUTLIER) cc_final: 0.6756 (t0) outliers start: 167 outliers final: 91 residues processed: 561 average time/residue: 0.2774 time to fit residues: 255.2338 Evaluate side-chains 428 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 325 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 758 LEU Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1001 VAL Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1358 ILE Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 353 ILE Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 61 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 378 ASP Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Chi-restraints excluded: chain Y residue 443 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 242 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 387 optimal weight: 5.9990 chunk 453 optimal weight: 0.9980 chunk 357 optimal weight: 4.9990 chunk 258 optimal weight: 0.6980 chunk 373 optimal weight: 3.9990 chunk 484 optimal weight: 2.9990 chunk 349 optimal weight: 2.9990 chunk 487 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 74 ASN G 98 GLN H 112 HIS M 730 GLN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 367 GLN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.123463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.094700 restraints weight = 111153.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094746 restraints weight = 100946.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094997 restraints weight = 74537.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095263 restraints weight = 65910.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.095362 restraints weight = 57162.268| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 45008 Z= 0.137 Angle : 0.631 10.838 62216 Z= 0.330 Chirality : 0.043 0.234 7288 Planarity : 0.004 0.056 6836 Dihedral : 23.178 152.120 8697 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 4.23 % Allowed : 14.50 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.11), residues: 4633 helix: 0.06 (0.11), residues: 2220 sheet: 0.11 (0.19), residues: 669 loop : -1.23 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 119 TYR 0.032 0.002 TYR M 699 PHE 0.030 0.002 PHE W 206 TRP 0.012 0.001 TRP R 199 HIS 0.009 0.001 HIS M1012 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (44998) covalent geometry : angle 0.62793 / 0.33 (62207) hydrogen bonds : bond 0.05115 / 3.11 ( 1999) hydrogen bonds : angle 4.62693 / 3.15 ( 5463) metal coordination : bond 0.01128 / 0.59 ( 8) metal coordination : angle 5.55468 / 2.88 ( 9) Misc. bond : bond 0.00133 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 378 time to evaluate : 1.576 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: B 59 GLU cc_start: 0.8052 (pp20) cc_final: 0.7648 (pp20) REVERT: B 72 ARG cc_start: 0.7409 (ttm110) cc_final: 0.6510 (mtp-110) REVERT: C 71 THR cc_start: 0.8922 (m) cc_final: 0.8501 (p) REVERT: C 77 LYS cc_start: 0.8551 (mmmm) cc_final: 0.7800 (mptt) REVERT: D 53 GLU cc_start: 0.7290 (tp30) cc_final: 0.7013 (mm-30) REVERT: D 92 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7208 (ptm160) REVERT: G 89 LYS cc_start: 0.6704 (mttt) cc_final: 0.6112 (ptmm) REVERT: H 62 MET cc_start: 0.5985 (tmm) cc_final: 0.5776 (ttt) REVERT: H 119 ARG cc_start: 0.7190 (ttp80) cc_final: 0.6915 (ttp80) REVERT: M 970 THR cc_start: 0.8165 (p) cc_final: 0.7687 (m) REVERT: M 980 MET cc_start: 0.7540 (mmt) cc_final: 0.6825 (ptp) REVERT: M 1082 ASN cc_start: 0.5979 (OUTLIER) cc_final: 0.5778 (m-40) REVERT: R 429 LYS cc_start: 0.7304 (tttt) cc_final: 0.6937 (mmmt) REVERT: S 220 MET cc_start: 0.6949 (ttp) cc_final: 0.6234 (tpt) REVERT: U 31 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7097 (mp) REVERT: U 301 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8228 (mp) REVERT: V 318 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8562 (tt) REVERT: W 65 THR cc_start: 0.7974 (p) cc_final: 0.7697 (t) REVERT: W 164 ASP cc_start: 0.7369 (m-30) cc_final: 0.6515 (p0) REVERT: X 312 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: X 377 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8166 (tmtt) REVERT: Y 310 ASN cc_start: 0.7758 (m-40) cc_final: 0.7465 (m110) outliers start: 169 outliers final: 103 residues processed: 516 average time/residue: 0.2724 time to fit residues: 233.1870 Evaluate side-chains 422 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 312 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 758 LEU Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1205 VAL Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1358 ILE Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain T residue 463 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 31 LEU Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 216 ASP Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 401 ASP Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 353 ILE Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 344 MET Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 35 optimal weight: 0.9990 chunk 99 optimal weight: 40.0000 chunk 311 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 414 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 332 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 chunk 499 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 336 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 74 ASN G 98 GLN M 730 GLN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 HIS U 223 GLN V 27 HIS V 263 GLN ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 408 GLN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.121155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.091989 restraints weight = 110087.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091948 restraints weight = 98780.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.092066 restraints weight = 77362.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.092390 restraints weight = 66134.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092452 restraints weight = 57545.496| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 45008 Z= 0.164 Angle : 0.649 9.945 62216 Z= 0.336 Chirality : 0.043 0.234 7288 Planarity : 0.004 0.051 6836 Dihedral : 23.115 153.316 8690 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 4.31 % Allowed : 15.31 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.12), residues: 4633 helix: 0.35 (0.11), residues: 2236 sheet: -0.02 (0.19), residues: 673 loop : -1.19 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 210 TYR 0.034 0.002 TYR M 699 PHE 0.052 0.002 PHE G 68 TRP 0.010 0.001 TRP M 760 HIS 0.006 0.001 HIS T 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (44998) covalent geometry : angle 0.64632 / 0.34 (62207) hydrogen bonds : bond 0.05190 / 3.16 ( 1999) hydrogen bonds : angle 4.44014 / 3.04 ( 5463) metal coordination : bond 0.00915 / 0.48 ( 8) metal coordination : angle 4.67971 / 2.40 ( 9) Misc. bond : bond 0.00153 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 343 time to evaluate : 1.654 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: B 59 GLU cc_start: 0.8104 (pp20) cc_final: 0.7841 (pp20) REVERT: C 71 THR cc_start: 0.8974 (m) cc_final: 0.8570 (p) REVERT: C 77 LYS cc_start: 0.8526 (mmmm) cc_final: 0.7777 (mptt) REVERT: D 53 GLU cc_start: 0.7310 (tp30) cc_final: 0.6895 (mm-30) REVERT: D 92 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6754 (mtm110) REVERT: E 30 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7564 (ttm170) REVERT: G 89 LYS cc_start: 0.6678 (mttt) cc_final: 0.6022 (ptmm) REVERT: H 49 LYS cc_start: 0.6390 (mmmt) cc_final: 0.5841 (mttp) REVERT: H 62 MET cc_start: 0.6135 (tmm) cc_final: 0.5893 (ttt) REVERT: H 95 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7481 (mmm160) REVERT: M 870 LEU cc_start: 0.7635 (mt) cc_final: 0.7284 (mt) REVERT: M 970 THR cc_start: 0.8141 (p) cc_final: 0.7558 (m) REVERT: M 980 MET cc_start: 0.7638 (mmt) cc_final: 0.6939 (ptt) REVERT: M 1082 ASN cc_start: 0.6140 (OUTLIER) cc_final: 0.5816 (t0) REVERT: M 1280 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7560 (tm-30) REVERT: S 220 MET cc_start: 0.6887 (ttp) cc_final: 0.6100 (tpt) REVERT: T 201 TYR cc_start: 0.7663 (t80) cc_final: 0.7365 (t80) REVERT: U 81 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7810 (ttpp) REVERT: U 175 MET cc_start: 0.8493 (tpp) cc_final: 0.8217 (tpp) REVERT: U 301 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8334 (mp) REVERT: V 318 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8694 (tt) REVERT: V 417 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: W 65 THR cc_start: 0.8079 (p) cc_final: 0.7783 (t) REVERT: W 175 MET cc_start: 0.8418 (mmt) cc_final: 0.8109 (tpp) REVERT: X 312 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: X 377 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8125 (tmtt) REVERT: Y 310 ASN cc_start: 0.7835 (m-40) cc_final: 0.7497 (m110) outliers start: 172 outliers final: 121 residues processed: 487 average time/residue: 0.2594 time to fit residues: 212.9532 Evaluate side-chains 433 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 304 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 758 LEU Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1006 THR Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1358 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain S residue 277 CYS Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain T residue 463 LEU Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 252 LEU Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 401 ASP Chi-restraints excluded: chain V residue 417 GLN Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 140 VAL Chi-restraints excluded: chain W residue 148 SER Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 353 ILE Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 297 ASP Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 344 MET Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 393 LEU Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 447 optimal weight: 0.6980 chunk 279 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 356 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 486 optimal weight: 2.9990 chunk 483 optimal weight: 0.9980 chunk 376 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 730 GLN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1356 HIS U 153 HIS ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN W 23 HIS W 299 HIS X 124 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.122490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093573 restraints weight = 109984.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093673 restraints weight = 97895.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.093704 restraints weight = 75783.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.093894 restraints weight = 73343.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.094371 restraints weight = 58858.745| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 45008 Z= 0.121 Angle : 0.606 10.244 62216 Z= 0.313 Chirality : 0.042 0.267 7288 Planarity : 0.004 0.050 6836 Dihedral : 23.009 153.350 8687 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.52 % Rotamer: Outliers : 3.71 % Allowed : 16.58 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 4633 helix: 0.65 (0.11), residues: 2233 sheet: 0.09 (0.19), residues: 672 loop : -1.08 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 431 TYR 0.036 0.001 TYR H 86 PHE 0.030 0.001 PHE G 68 TRP 0.010 0.001 TRP M 760 HIS 0.007 0.001 HIS U 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (44998) covalent geometry : angle 0.60425 / 0.31 (62207) hydrogen bonds : bond 0.04741 / 2.85 ( 1999) hydrogen bonds : angle 4.20519 / 2.87 ( 5463) metal coordination : bond 0.00703 / 0.38 ( 8) metal coordination : angle 3.91797 / 2.03 ( 9) Misc. bond : bond 0.00053 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 340 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.8084 (pp20) cc_final: 0.7845 (pp20) REVERT: C 71 THR cc_start: 0.8963 (m) cc_final: 0.8670 (p) REVERT: C 77 LYS cc_start: 0.8490 (mmmm) cc_final: 0.7773 (mptt) REVERT: D 53 GLU cc_start: 0.7291 (tp30) cc_final: 0.6900 (mm-30) REVERT: D 77 LYS cc_start: 0.6688 (mmtm) cc_final: 0.6026 (pttt) REVERT: D 92 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6970 (mtm110) REVERT: E 30 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7495 (ttm170) REVERT: F 37 ARG cc_start: 0.7875 (mmm160) cc_final: 0.6685 (ttm110) REVERT: G 89 LYS cc_start: 0.6643 (mttt) cc_final: 0.6232 (ptmm) REVERT: H 49 LYS cc_start: 0.6183 (mmmt) cc_final: 0.5518 (mttp) REVERT: H 62 MET cc_start: 0.6142 (tmm) cc_final: 0.5912 (ttt) REVERT: M 870 LEU cc_start: 0.7542 (mt) cc_final: 0.7284 (mt) REVERT: M 970 THR cc_start: 0.8111 (p) cc_final: 0.7488 (m) REVERT: M 980 MET cc_start: 0.7631 (mmt) cc_final: 0.6854 (ptp) REVERT: M 1082 ASN cc_start: 0.6119 (OUTLIER) cc_final: 0.5801 (t0) REVERT: S 170 GLU cc_start: 0.7079 (tp30) cc_final: 0.6784 (tp30) REVERT: S 220 MET cc_start: 0.6865 (ttp) cc_final: 0.6057 (tpt) REVERT: U 81 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7636 (ttpp) REVERT: U 175 MET cc_start: 0.8439 (tpp) cc_final: 0.8132 (tpp) REVERT: U 283 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: U 411 MET cc_start: 0.7862 (tpp) cc_final: 0.7608 (tpp) REVERT: V 137 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7273 (ptpp) REVERT: V 272 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9026 (tt) REVERT: V 318 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8701 (tt) REVERT: W 65 THR cc_start: 0.8030 (p) cc_final: 0.7758 (t) REVERT: W 86 MET cc_start: 0.8119 (tpt) cc_final: 0.7825 (tpp) REVERT: W 175 MET cc_start: 0.8434 (mmt) cc_final: 0.8142 (tpp) REVERT: X 312 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: X 377 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7984 (tmtt) REVERT: Y 58 LEU cc_start: 0.9105 (tp) cc_final: 0.8894 (tt) REVERT: Y 310 ASN cc_start: 0.7728 (m-40) cc_final: 0.7358 (m110) REVERT: Y 411 MET cc_start: 0.7301 (tpp) cc_final: 0.7073 (mtp) outliers start: 148 outliers final: 103 residues processed: 466 average time/residue: 0.2711 time to fit residues: 211.3677 Evaluate side-chains 410 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 298 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1358 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain S residue 277 CYS Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 137 LYS Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 417 GLN Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 353 ILE Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 286 GLN Chi-restraints excluded: chain X residue 297 ASP Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 313 optimal weight: 0.7980 chunk 105 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 262 optimal weight: 0.0980 chunk 463 optimal weight: 0.0670 chunk 11 optimal weight: 10.0000 chunk 56 optimal weight: 0.0870 chunk 96 optimal weight: 30.0000 chunk 236 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 811 HIS ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN Y 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.122243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.092640 restraints weight = 110389.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.092090 restraints weight = 85777.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092349 restraints weight = 66639.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.092563 restraints weight = 60782.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092661 restraints weight = 50364.762| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 45008 Z= 0.120 Angle : 0.595 9.993 62216 Z= 0.309 Chirality : 0.041 0.235 7288 Planarity : 0.004 0.061 6836 Dihedral : 22.936 153.734 8686 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.78 % Allowed : 16.91 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 4633 helix: 0.83 (0.11), residues: 2228 sheet: 0.07 (0.19), residues: 671 loop : -1.03 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 100 TYR 0.037 0.001 TYR D 88 PHE 0.032 0.001 PHE G 68 TRP 0.008 0.001 TRP M 760 HIS 0.006 0.001 HIS X 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (44998) covalent geometry : angle 0.59368 / 0.31 (62207) hydrogen bonds : bond 0.04671 / 2.81 ( 1999) hydrogen bonds : angle 4.11006 / 2.80 ( 5463) metal coordination : bond 0.00690 / 0.37 ( 8) metal coordination : angle 3.66339 / 1.89 ( 9) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 315 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6237 (t80) cc_final: 0.5950 (t80) REVERT: B 59 GLU cc_start: 0.8041 (pp20) cc_final: 0.7789 (pp20) REVERT: C 71 THR cc_start: 0.8988 (m) cc_final: 0.8595 (p) REVERT: C 77 LYS cc_start: 0.8441 (mmmm) cc_final: 0.7677 (mptt) REVERT: D 53 GLU cc_start: 0.7385 (tp30) cc_final: 0.6917 (mm-30) REVERT: D 77 LYS cc_start: 0.6554 (mmtm) cc_final: 0.5903 (pttt) REVERT: D 92 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.6928 (mtm110) REVERT: E 30 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7532 (ttm170) REVERT: G 89 LYS cc_start: 0.6546 (mttt) cc_final: 0.6116 (ptmm) REVERT: H 49 LYS cc_start: 0.6375 (mmmt) cc_final: 0.5701 (mttp) REVERT: H 95 ARG cc_start: 0.7640 (mmm160) cc_final: 0.7204 (mtt90) REVERT: H 108 GLU cc_start: 0.6986 (mp0) cc_final: 0.6454 (mp0) REVERT: M 870 LEU cc_start: 0.7627 (mt) cc_final: 0.7358 (mt) REVERT: M 970 THR cc_start: 0.8084 (p) cc_final: 0.7446 (m) REVERT: M 980 MET cc_start: 0.7732 (mmt) cc_final: 0.6825 (ptp) REVERT: M 1082 ASN cc_start: 0.6056 (OUTLIER) cc_final: 0.5776 (t0) REVERT: R 147 MET cc_start: 0.6395 (mmm) cc_final: 0.5929 (tpt) REVERT: R 215 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7704 (ttmm) REVERT: S 170 GLU cc_start: 0.7152 (tp30) cc_final: 0.6903 (tp30) REVERT: S 220 MET cc_start: 0.6869 (ttp) cc_final: 0.6007 (tpt) REVERT: U 81 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8200 (ttpp) REVERT: U 283 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: U 300 MET cc_start: 0.7138 (mtm) cc_final: 0.6923 (mtt) REVERT: V 137 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7252 (ptpp) REVERT: V 272 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9022 (tt) REVERT: V 318 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8643 (tt) REVERT: W 65 THR cc_start: 0.8003 (p) cc_final: 0.7793 (t) REVERT: W 175 MET cc_start: 0.8427 (mmt) cc_final: 0.8133 (tpp) REVERT: X 312 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: X 377 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7973 (tmmt) REVERT: Y 58 LEU cc_start: 0.9113 (tp) cc_final: 0.8901 (tt) REVERT: Y 310 ASN cc_start: 0.7723 (m-40) cc_final: 0.7379 (m110) REVERT: Y 411 MET cc_start: 0.7361 (tpp) cc_final: 0.7141 (mtp) outliers start: 151 outliers final: 110 residues processed: 445 average time/residue: 0.2608 time to fit residues: 196.6144 Evaluate side-chains 415 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 295 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 811 HIS Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1205 VAL Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1358 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 215 LYS Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain S residue 277 CYS Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 137 LYS Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 216 ASP Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 286 GLN Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 344 MET Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 269 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 413 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 365 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 40.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 42 GLN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.121159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092391 restraints weight = 109775.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092660 restraints weight = 96562.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092559 restraints weight = 82196.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.093088 restraints weight = 69183.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.093067 restraints weight = 59216.626| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 45008 Z= 0.138 Angle : 0.600 10.177 62216 Z= 0.312 Chirality : 0.042 0.223 7288 Planarity : 0.004 0.050 6836 Dihedral : 22.898 154.278 8683 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.22 % Rotamer: Outliers : 3.73 % Allowed : 17.31 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 4633 helix: 0.86 (0.11), residues: 2234 sheet: 0.01 (0.19), residues: 673 loop : -1.01 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 100 TYR 0.026 0.001 TYR H 86 PHE 0.028 0.001 PHE G 68 TRP 0.007 0.001 TRP M 706 HIS 0.031 0.001 HIS M 811 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (44998) covalent geometry : angle 0.59863 / 0.31 (62207) hydrogen bonds : bond 0.04745 / 2.85 ( 1999) hydrogen bonds : angle 4.09620 / 2.80 ( 5463) metal coordination : bond 0.00790 / 0.42 ( 8) metal coordination : angle 3.59069 / 1.87 ( 9) Misc. bond : bond 0.00097 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 316 time to evaluate : 1.611 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: B 59 GLU cc_start: 0.8103 (pp20) cc_final: 0.7870 (pp20) REVERT: C 71 THR cc_start: 0.8956 (m) cc_final: 0.8592 (p) REVERT: C 77 LYS cc_start: 0.8414 (mmmm) cc_final: 0.7692 (mptt) REVERT: C 97 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7645 (tm) REVERT: D 53 GLU cc_start: 0.7397 (tp30) cc_final: 0.6968 (mm-30) REVERT: D 77 LYS cc_start: 0.6424 (mmtm) cc_final: 0.5949 (pttt) REVERT: D 92 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.6959 (mtp85) REVERT: G 89 LYS cc_start: 0.6680 (mttt) cc_final: 0.6223 (ptmm) REVERT: M 870 LEU cc_start: 0.7556 (mt) cc_final: 0.7282 (mt) REVERT: M 970 THR cc_start: 0.7976 (p) cc_final: 0.7287 (m) REVERT: M 980 MET cc_start: 0.7725 (mmt) cc_final: 0.6901 (ptp) REVERT: M 1069 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7437 (ptpp) REVERT: M 1082 ASN cc_start: 0.6121 (OUTLIER) cc_final: 0.5848 (t0) REVERT: M 1339 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: R 147 MET cc_start: 0.6445 (mmm) cc_final: 0.6143 (tpt) REVERT: S 170 GLU cc_start: 0.6991 (tp30) cc_final: 0.6738 (tp30) REVERT: S 220 MET cc_start: 0.6927 (ttp) cc_final: 0.6116 (tpt) REVERT: T 201 TYR cc_start: 0.7650 (t80) cc_final: 0.7337 (t80) REVERT: T 282 GLU cc_start: 0.7556 (tp30) cc_final: 0.7292 (tp30) REVERT: U 81 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7670 (ttpp) REVERT: U 175 MET cc_start: 0.8463 (tpp) cc_final: 0.8231 (mpp) REVERT: U 283 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: V 77 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8143 (mt) REVERT: V 318 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8568 (tt) REVERT: W 65 THR cc_start: 0.8100 (p) cc_final: 0.7891 (t) REVERT: W 175 MET cc_start: 0.8400 (mmt) cc_final: 0.8135 (tpp) REVERT: X 312 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: X 377 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8025 (tmmt) REVERT: Y 58 LEU cc_start: 0.9102 (tp) cc_final: 0.8890 (tt) REVERT: Y 310 ASN cc_start: 0.7792 (m-40) cc_final: 0.7425 (m110) outliers start: 149 outliers final: 117 residues processed: 441 average time/residue: 0.2652 time to fit residues: 196.6933 Evaluate side-chains 425 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 297 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1069 LYS Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1205 VAL Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1358 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain S residue 277 CYS Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 244 ILE Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 401 ASP Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 286 GLN Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 55 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 487 optimal weight: 0.9990 chunk 485 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 chunk 339 optimal weight: 0.9990 chunk 440 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 289 ASN ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.120145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.090465 restraints weight = 110101.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089841 restraints weight = 88263.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090043 restraints weight = 70533.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090262 restraints weight = 60165.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.090360 restraints weight = 52402.087| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 45008 Z= 0.154 Angle : 0.615 10.416 62216 Z= 0.321 Chirality : 0.042 0.225 7288 Planarity : 0.004 0.049 6836 Dihedral : 22.876 154.885 8683 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.83 % Allowed : 17.64 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 4633 helix: 0.87 (0.11), residues: 2223 sheet: -0.06 (0.19), residues: 675 loop : -0.97 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 100 TYR 0.026 0.001 TYR H 86 PHE 0.025 0.002 PHE G 68 TRP 0.018 0.001 TRP R 199 HIS 0.006 0.001 HIS M 811 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (44998) covalent geometry : angle 0.61385 / 0.32 (62207) hydrogen bonds : bond 0.04816 / 2.91 ( 1999) hydrogen bonds : angle 4.11264 / 2.81 ( 5463) metal coordination : bond 0.00912 / 0.48 ( 8) metal coordination : angle 3.66274 / 1.91 ( 9) Misc. bond : bond 0.00107 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 304 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.8106 (pp20) cc_final: 0.7847 (pp20) REVERT: C 71 THR cc_start: 0.8942 (m) cc_final: 0.8472 (p) REVERT: C 77 LYS cc_start: 0.8388 (mmmm) cc_final: 0.7638 (mptt) REVERT: D 53 GLU cc_start: 0.7522 (tp30) cc_final: 0.7006 (mm-30) REVERT: D 77 LYS cc_start: 0.6315 (mmtm) cc_final: 0.5828 (pttt) REVERT: D 92 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6944 (mtp85) REVERT: G 89 LYS cc_start: 0.6355 (mttt) cc_final: 0.6015 (ptmm) REVERT: H 49 LYS cc_start: 0.6320 (mmmt) cc_final: 0.5639 (mttp) REVERT: H 95 ARG cc_start: 0.7422 (mmm160) cc_final: 0.7149 (mtt90) REVERT: M 970 THR cc_start: 0.8047 (p) cc_final: 0.7387 (m) REVERT: M 980 MET cc_start: 0.7833 (mmt) cc_final: 0.6887 (ptp) REVERT: M 1069 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7465 (ptpp) REVERT: M 1082 ASN cc_start: 0.6096 (OUTLIER) cc_final: 0.5834 (t0) REVERT: M 1339 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6412 (m-80) REVERT: R 238 MET cc_start: 0.8148 (mmm) cc_final: 0.7938 (mmm) REVERT: R 279 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.5215 (t80) REVERT: S 170 GLU cc_start: 0.7207 (tp30) cc_final: 0.6941 (tp30) REVERT: S 220 MET cc_start: 0.6937 (ttp) cc_final: 0.6031 (tpt) REVERT: T 201 TYR cc_start: 0.7697 (t80) cc_final: 0.7420 (t80) REVERT: U 81 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7770 (ttpp) REVERT: U 164 ASP cc_start: 0.6992 (t70) cc_final: 0.6626 (t70) REVERT: U 175 MET cc_start: 0.8389 (tpp) cc_final: 0.7872 (tpp) REVERT: U 283 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: V 51 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.6219 (mp-120) REVERT: V 77 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8392 (mp) REVERT: W 65 THR cc_start: 0.8188 (p) cc_final: 0.7980 (t) REVERT: W 175 MET cc_start: 0.8473 (mmt) cc_final: 0.8185 (tpp) REVERT: X 312 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: X 377 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8035 (tmmt) REVERT: Y 310 ASN cc_start: 0.7792 (m-40) cc_final: 0.7408 (m110) outliers start: 153 outliers final: 119 residues processed: 432 average time/residue: 0.2558 time to fit residues: 186.0342 Evaluate side-chains 420 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 290 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1069 LYS Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1205 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1358 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 279 PHE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 400 MET Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain S residue 277 CYS Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 244 ILE Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 401 ASP Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 370 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 256 optimal weight: 7.9990 chunk 332 optimal weight: 5.9990 chunk 346 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 328 optimal weight: 2.9990 chunk 477 optimal weight: 1.9990 chunk 443 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 42 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 808 GLN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1082 ASN M1285 HIS M1352 GLN ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 230 GLN Y 223 GLN Y 299 HIS ** Y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 443 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.116755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.087574 restraints weight = 109582.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087346 restraints weight = 100338.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.087376 restraints weight = 81809.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.087734 restraints weight = 71590.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.087796 restraints weight = 61738.130| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 45008 Z= 0.250 Angle : 0.735 11.148 62216 Z= 0.381 Chirality : 0.046 0.273 7288 Planarity : 0.005 0.060 6836 Dihedral : 22.990 156.484 8679 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 3.76 % Allowed : 17.96 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.12), residues: 4633 helix: 0.55 (0.11), residues: 2187 sheet: -0.39 (0.19), residues: 682 loop : -1.12 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 100 TYR 0.029 0.002 TYR H 86 PHE 0.037 0.003 PHE G 68 TRP 0.015 0.002 TRP R 199 HIS 0.009 0.002 HIS H 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (44998) covalent geometry : angle 0.73231 / 0.38 (62207) hydrogen bonds : bond 0.05745 / 3.54 ( 1999) hydrogen bonds : angle 4.50489 / 3.09 ( 5463) metal coordination : bond 0.01366 / 0.74 ( 8) metal coordination : angle 4.77504 / 2.52 ( 9) Misc. bond : bond 0.00212 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 301 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.8155 (pp20) cc_final: 0.7877 (pp20) REVERT: C 71 THR cc_start: 0.8961 (m) cc_final: 0.8580 (p) REVERT: C 77 LYS cc_start: 0.8458 (mmmm) cc_final: 0.7721 (mptt) REVERT: D 53 GLU cc_start: 0.7579 (tp30) cc_final: 0.7127 (mm-30) REVERT: D 92 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7020 (mtp85) REVERT: E 57 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7416 (tm-30) REVERT: F 37 ARG cc_start: 0.8063 (mmm160) cc_final: 0.6767 (ttm110) REVERT: F 58 TYR cc_start: 0.6670 (t80) cc_final: 0.5823 (t80) REVERT: M 870 LEU cc_start: 0.7563 (mt) cc_final: 0.7255 (mt) REVERT: M 980 MET cc_start: 0.7871 (mmt) cc_final: 0.6847 (mmt) REVERT: M 1069 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7355 (ptpp) REVERT: M 1118 MET cc_start: 0.8039 (mmm) cc_final: 0.7532 (mmt) REVERT: M 1339 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: S 170 GLU cc_start: 0.7116 (tp30) cc_final: 0.6848 (tp30) REVERT: S 220 MET cc_start: 0.6924 (ttp) cc_final: 0.6172 (tpt) REVERT: T 278 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8295 (p) REVERT: U 81 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.7810 (ttpp) REVERT: U 175 MET cc_start: 0.8362 (tpp) cc_final: 0.7926 (tpp) REVERT: U 283 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: U 301 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8436 (mp) REVERT: V 51 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.6312 (mp-120) REVERT: W 175 MET cc_start: 0.8582 (mmt) cc_final: 0.8303 (tpp) REVERT: X 125 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7857 (t80) REVERT: X 312 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: X 377 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8083 (tmmt) REVERT: Y 220 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8121 (pmt170) REVERT: Y 310 ASN cc_start: 0.7963 (m-40) cc_final: 0.7571 (m110) outliers start: 150 outliers final: 119 residues processed: 428 average time/residue: 0.2568 time to fit residues: 186.4740 Evaluate side-chains 416 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 285 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1006 THR Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1069 LYS Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1205 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1358 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 400 MET Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 244 ILE Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 228 GLU Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 401 ASP Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 313 LEU Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 455 optimal weight: 0.6980 chunk 255 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 chunk 199 optimal weight: 0.9980 chunk 351 optimal weight: 0.1980 chunk 76 optimal weight: 10.0000 chunk 440 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 chunk 471 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 74 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 223 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.117071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088022 restraints weight = 109578.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088128 restraints weight = 97954.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088106 restraints weight = 82291.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088458 restraints weight = 71456.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088505 restraints weight = 61736.359| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 45008 Z= 0.199 Angle : 0.788 59.192 62216 Z= 0.419 Chirality : 0.045 0.461 7288 Planarity : 0.005 0.059 6836 Dihedral : 22.992 156.421 8673 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 3.43 % Allowed : 18.16 % Favored : 78.41 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.12), residues: 4633 helix: 0.57 (0.11), residues: 2187 sheet: -0.42 (0.19), residues: 680 loop : -1.14 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG S 44 TYR 0.082 0.002 TYR F 58 PHE 0.026 0.002 PHE R 120 TRP 0.012 0.002 TRP R 199 HIS 0.007 0.001 HIS V 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (44998) covalent geometry : angle 0.78585 / 0.42 (62207) hydrogen bonds : bond 0.05630 / 3.46 ( 1999) hydrogen bonds : angle 4.48191 / 3.07 ( 5463) metal coordination : bond 0.01257 / 0.66 ( 8) metal coordination : angle 4.79897 / 2.53 ( 9) Misc. bond : bond 0.00131 / 0.06 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 285 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.8154 (pp20) cc_final: 0.7887 (pp20) REVERT: C 71 THR cc_start: 0.8953 (m) cc_final: 0.8582 (p) REVERT: C 77 LYS cc_start: 0.8464 (mmmm) cc_final: 0.7745 (mptt) REVERT: D 53 GLU cc_start: 0.7541 (tp30) cc_final: 0.7121 (mm-30) REVERT: D 92 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7003 (mtp85) REVERT: E 57 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7343 (tm-30) REVERT: F 37 ARG cc_start: 0.7996 (mmm160) cc_final: 0.6747 (ttm110) REVERT: M 870 LEU cc_start: 0.7558 (mt) cc_final: 0.7235 (mt) REVERT: M 980 MET cc_start: 0.7834 (mmt) cc_final: 0.6809 (mmt) REVERT: M 1069 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7338 (ptpp) REVERT: M 1118 MET cc_start: 0.8044 (mmm) cc_final: 0.7515 (mmt) REVERT: M 1339 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6360 (m-80) REVERT: S 220 MET cc_start: 0.6915 (ttp) cc_final: 0.6202 (tpt) REVERT: U 81 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7794 (ttpp) REVERT: U 175 MET cc_start: 0.8355 (tpp) cc_final: 0.8047 (mpp) REVERT: U 283 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: U 301 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8439 (mp) REVERT: V 51 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.6303 (mp-120) REVERT: W 175 MET cc_start: 0.8568 (mmt) cc_final: 0.8290 (tpp) REVERT: X 125 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7885 (t80) REVERT: X 312 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: X 377 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8078 (tmmt) REVERT: Y 220 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8095 (pmt170) REVERT: Y 310 ASN cc_start: 0.7920 (m-40) cc_final: 0.7539 (m110) outliers start: 137 outliers final: 123 residues processed: 401 average time/residue: 0.2539 time to fit residues: 173.2261 Evaluate side-chains 418 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 284 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 978 ASN Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1069 LYS Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1205 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1358 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 400 MET Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 244 ILE Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 228 GLU Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 252 LEU Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 401 ASP Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 240 SER Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 313 LEU Chi-restraints excluded: chain Y residue 325 THR Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 264 optimal weight: 0.0040 chunk 172 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 435 optimal weight: 6.9990 chunk 367 optimal weight: 5.9990 chunk 439 optimal weight: 2.9990 chunk 316 optimal weight: 0.0170 chunk 236 optimal weight: 1.9990 chunk 392 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.7832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 223 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.117075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088033 restraints weight = 110309.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088135 restraints weight = 99224.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.088094 restraints weight = 82602.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088448 restraints weight = 70789.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088488 restraints weight = 61808.144| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 45008 Z= 0.199 Angle : 0.788 59.192 62216 Z= 0.419 Chirality : 0.045 0.461 7288 Planarity : 0.005 0.059 6836 Dihedral : 22.992 156.421 8673 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 3.36 % Allowed : 18.19 % Favored : 78.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.12), residues: 4633 helix: 0.57 (0.11), residues: 2187 sheet: -0.42 (0.19), residues: 680 loop : -1.14 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG S 44 TYR 0.082 0.002 TYR F 58 PHE 0.026 0.002 PHE R 120 TRP 0.012 0.002 TRP R 199 HIS 0.007 0.001 HIS V 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (44998) covalent geometry : angle 0.78585 / 0.42 (62207) hydrogen bonds : bond 0.05630 / 3.46 ( 1999) hydrogen bonds : angle 4.48191 / 3.07 ( 5463) metal coordination : bond 0.01257 / 0.66 ( 8) metal coordination : angle 4.79897 / 2.53 ( 9) Misc. bond : bond 0.00131 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7368.07 seconds wall clock time: 128 minutes 20.29 seconds (7700.29 seconds total)