Starting phenix.real_space_refine on Wed Aug 27 01:18:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gej_4395/08_2025/6gej_4395.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gej_4395/08_2025/6gej_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_4395/08_2025/6gej_4395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gej_4395/08_2025/6gej_4395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gej_4395/08_2025/6gej_4395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gej_4395/08_2025/6gej_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.21, per 1000 atoms: 0.19 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 6.41 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: 12.43 Time building geometry restraints manager: 4.46 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=" F1 BEF M1602 " pdb="BE BEF M1602 " ideal model delta sigma weight residual 1.476 1.535 -0.059 2.00e-02 2.50e+03 8.56e+00 ... (remaining 44993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 61708 2.56 - 5.12: 437 5.12 - 7.68: 55 7.68 - 10.25: 2 10.25 - 12.81: 5 Bond angle restraints: 62207 Sorted by residual: 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=" F2 BEF M1602 " pdb="BE BEF M1602 " pdb=" F3 BEF M1602 " ideal model delta sigma weight residual 119.96 107.15 12.81 3.00e+00 1.11e-01 1.82e+01 angle pdb=" F2 BEF R 502 " pdb="BE BEF R 502 " pdb=" F3 BEF R 502 " ideal model delta sigma weight residual 119.96 107.27 12.69 3.00e+00 1.11e-01 1.79e+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: 5406 0.035 - 0.069: 1316 0.069 - 0.104: 406 0.104 - 0.139: 158 0.139 - 0.173: 2 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=" 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 chirality pdb=" CA VAL T 359 " pdb=" N VAL T 359 " pdb=" C VAL T 359 " pdb=" CB VAL T 359 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-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: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 49.420 Find NCS groups from input model: 0.860 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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= 0.630 Angle : 0.668 33.315 62216 Z= 0.369 Chirality : 0.037 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 aren 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 covalent geometry : bond 0.00254 (44998) covalent geometry : angle 0.62068 (62207) hydrogen bonds : bond 0.16827 ( 1999) hydrogen bonds : angle 7.96102 ( 5463) metal coordination : bond 0.30947 ( 8) metal coordination : angle 20.55390 ( 9) Misc. bond : bond 0.89958 ( 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 : 1.284 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: 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: 0.4196 (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: 0.8004 (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: 0.6495 (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 43 ARG cc_start: 0.5814 (tpp80) cc_final: 0.5521 (ttp-170) 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: 0.6729 (m-80) REVERT: F 30 ARG cc_start: 0.4050 (mmt90) cc_final: 0.3668 (mpt180) REVERT: F 36 ARG cc_start: 0.6370 (ttm110) cc_final: 0.5966 (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: 0.5342 (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: 0.6858 (ttmm) REVERT: H 70 ASN cc_start: 0.7406 (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: 0.7365 (mmt) cc_final: 0.6267 (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: 0.7049 (OUTLIER) cc_final: 0.6782 (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: 0.8180 (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: 0.7652 (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: 0.7974 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: W 149 ILE cc_start: 0.7536 (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: 0.7918 (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: 0.2637 time to fit residues: 451.4447 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 : 1.038 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 39 HIS E 42 GLN E 74 ASN E 115 ASN F 39 ASN ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS H 112 HIS M 716 ASN M 730 GLN 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 R 251 GLN R 374 GLN S 176 GLN T 256 ASN T 271 GLN U 119 GLN U 252 GLN U 451 GLN V 27 HIS V 124 ASN V 263 GLN 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 299 HIS Y 443 ASN Y 451 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.122483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093483 restraints weight = 111270.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093697 restraints weight = 92795.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.093746 restraints weight = 70961.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094112 restraints weight = 62696.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094182 restraints weight = 54000.209| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 45008 Z= 0.191 Angle : 0.693 12.140 62216 Z= 0.358 Chirality : 0.043 0.225 7288 Planarity : 0.005 0.057 6836 Dihedral : 23.093 151.542 8728 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 4.61 % Allowed : 13.93 % Favored : 81.46 % 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 aren not related in a simple way. whole: -1.21 (0.11), residues: 4633 helix: -0.53 (0.10), residues: 2212 sheet: -0.02 (0.18), residues: 678 loop : -1.30 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 49 TYR 0.021 0.002 TYR G 86 PHE 0.022 0.002 PHE G 68 TRP 0.021 0.002 TRP R 199 HIS 0.009 0.001 HIS E 32 Details of bonding type rmsd covalent geometry : bond 0.00441 (44998) covalent geometry : angle 0.68921 (62207) hydrogen bonds : bond 0.05422 ( 1999) hydrogen bonds : angle 4.91475 ( 5463) metal coordination : bond 0.01286 ( 8) metal coordination : angle 6.24816 ( 9) Misc. bond : bond 0.00925 ( 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 617 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 433 time to evaluate : 1.778 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 53 ARG cc_start: 0.7004 (ttm170) cc_final: 0.6788 (mtt90) REVERT: C 62 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8341 (mm) REVERT: C 71 THR cc_start: 0.8943 (m) cc_final: 0.8607 (p) REVERT: C 77 LYS cc_start: 0.8548 (mmmm) cc_final: 0.7803 (mptt) REVERT: D 53 GLU cc_start: 0.7328 (tp30) cc_final: 0.6999 (mm-30) REVERT: D 92 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6707 (mtp-110) REVERT: G 89 LYS cc_start: 0.6623 (mttt) cc_final: 0.6033 (ptmm) REVERT: H 49 LYS cc_start: 0.6707 (mmmt) cc_final: 0.6092 (mttp) REVERT: M 970 THR cc_start: 0.8248 (p) cc_final: 0.7878 (m) REVERT: M 980 MET cc_start: 0.7421 (mmt) cc_final: 0.6732 (ptt) REVERT: M 987 MET cc_start: 0.7673 (tpp) cc_final: 0.7445 (tpp) REVERT: R 429 LYS cc_start: 0.7294 (tttt) cc_final: 0.6853 (mmmt) REVERT: S 170 GLU cc_start: 0.7273 (tp30) cc_final: 0.7072 (tp30) REVERT: S 179 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.6181 (p90) REVERT: S 220 MET cc_start: 0.6822 (ttp) cc_final: 0.6121 (tpt) REVERT: U 31 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7017 (mp) REVERT: U 81 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8019 (ttmm) REVERT: U 301 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8246 (mp) REVERT: V 70 MET cc_start: 0.7407 (mmm) cc_final: 0.7089 (mmm) REVERT: V 220 THR cc_start: 0.7156 (m) cc_final: 0.6947 (p) REVERT: V 344 MET cc_start: 0.9404 (mmm) cc_final: 0.9076 (mmm) REVERT: W 164 ASP cc_start: 0.7428 (m-30) cc_final: 0.6554 (p0) REVERT: X 85 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8613 (ttmm) REVERT: X 312 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: X 377 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8242 (tmtt) REVERT: Y 310 ASN cc_start: 0.7885 (m-40) cc_final: 0.7635 (m110) REVERT: Y 325 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9084 (t) REVERT: Y 443 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6726 (t0) outliers start: 184 outliers final: 96 residues processed: 591 average time/residue: 0.2826 time to fit residues: 271.4842 Evaluate side-chains 430 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 323 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER 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 93 SER Chi-restraints excluded: chain G residue 95 ARG 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 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 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 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 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 R residue 316 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 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 31 LEU 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 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 237 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain V residue 302 GLU 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 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 196 SER 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 85 LYS 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 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 377 LYS 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: 8.9990 chunk 45 optimal weight: 0.8980 chunk 387 optimal weight: 7.9990 chunk 453 optimal weight: 2.9990 chunk 357 optimal weight: 0.8980 chunk 258 optimal weight: 0.6980 chunk 373 optimal weight: 1.9990 chunk 484 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 487 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 155 GLN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 230 GLN W 299 HIS W 408 GLN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.122072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093160 restraints weight = 110600.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093088 restraints weight = 99393.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.093262 restraints weight = 76905.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093527 restraints weight = 68074.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093612 restraints weight = 59142.932| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45008 Z= 0.148 Angle : 0.622 10.448 62216 Z= 0.321 Chirality : 0.041 0.209 7288 Planarity : 0.004 0.055 6836 Dihedral : 22.944 152.461 8695 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 4.11 % Allowed : 14.80 % Favored : 81.09 % 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 aren not related in a simple way. whole: -0.58 (0.12), residues: 4633 helix: 0.19 (0.11), residues: 2220 sheet: 0.03 (0.19), residues: 677 loop : -1.19 (0.13), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 119 TYR 0.027 0.001 TYR D 88 PHE 0.018 0.002 PHE M1317 TRP 0.013 0.001 TRP M 818 HIS 0.006 0.001 HIS M1012 Details of bonding type rmsd covalent geometry : bond 0.00337 (44998) covalent geometry : angle 0.61898 (62207) hydrogen bonds : bond 0.04807 ( 1999) hydrogen bonds : angle 4.48227 ( 5463) metal coordination : bond 0.00871 ( 8) metal coordination : angle 4.97064 ( 9) Misc. bond : bond 0.00127 ( 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 526 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 362 time to evaluate : 2.269 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 53 ARG cc_start: 0.6918 (ttm170) cc_final: 0.6703 (mtt90) REVERT: C 71 THR cc_start: 0.9032 (m) cc_final: 0.8618 (p) REVERT: C 77 LYS cc_start: 0.8523 (mmmm) cc_final: 0.7779 (mptt) REVERT: D 53 GLU cc_start: 0.7257 (tp30) cc_final: 0.6869 (mm-30) REVERT: D 77 LYS cc_start: 0.6665 (mmtm) cc_final: 0.5980 (pttm) REVERT: D 92 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6671 (mtp85) REVERT: F 58 TYR cc_start: 0.6416 (t80) cc_final: 0.5993 (t80) REVERT: F 96 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7443 (tppt) REVERT: G 89 LYS cc_start: 0.6682 (mttt) cc_final: 0.6167 (ptmm) REVERT: H 49 LYS cc_start: 0.6503 (mmmt) cc_final: 0.5822 (mttp) REVERT: H 86 TYR cc_start: 0.6643 (m-10) cc_final: 0.6254 (m-80) REVERT: M 777 TYR cc_start: 0.7198 (m-80) cc_final: 0.6930 (m-10) REVERT: M 870 LEU cc_start: 0.7632 (mt) cc_final: 0.7313 (mt) REVERT: M 970 THR cc_start: 0.8213 (p) cc_final: 0.7749 (m) REVERT: M 980 MET cc_start: 0.7596 (mmt) cc_final: 0.6826 (ptp) REVERT: S 220 MET cc_start: 0.7008 (ttp) cc_final: 0.6308 (tpt) REVERT: U 81 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7725 (ttpp) REVERT: U 175 MET cc_start: 0.8610 (tpp) cc_final: 0.8190 (mpp) REVERT: U 301 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8313 (mp) REVERT: V 318 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8614 (tt) REVERT: W 65 THR cc_start: 0.8076 (p) cc_final: 0.7796 (t) REVERT: W 164 ASP cc_start: 0.7549 (m-30) cc_final: 0.6658 (p0) REVERT: W 175 MET cc_start: 0.8450 (mmt) cc_final: 0.8055 (tpp) REVERT: X 85 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8281 (mtmm) REVERT: X 312 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: X 377 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8090 (tmtt) REVERT: X 417 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: Y 310 ASN cc_start: 0.7775 (m-40) cc_final: 0.7476 (m110) outliers start: 164 outliers final: 99 residues processed: 502 average time/residue: 0.2771 time to fit residues: 229.0921 Evaluate side-chains 426 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 318 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain G residue 71 ASP 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 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 1117 ASP Chi-restraints excluded: chain M residue 1197 LEU Chi-restraints excluded: chain M residue 1205 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 53 SER Chi-restraints excluded: chain R residue 100 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 278 ASP Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 126 VAL 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 T residue 40 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 88 LEU 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 45 VAL 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 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 V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU 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 286 GLN 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 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain V residue 436 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 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 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 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 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 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: 0.7980 chunk 99 optimal weight: 10.0000 chunk 311 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 414 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 332 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 499 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN M 811 HIS ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1285 HIS ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 367 GLN S 97 GLN U 25 HIS U 153 HIS U 223 GLN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.117732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.088337 restraints weight = 109967.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088163 restraints weight = 100631.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.088207 restraints weight = 80908.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088667 restraints weight = 68961.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088681 restraints weight = 59697.828| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 45008 Z= 0.222 Angle : 0.703 10.655 62216 Z= 0.365 Chirality : 0.044 0.210 7288 Planarity : 0.005 0.055 6836 Dihedral : 22.965 154.299 8692 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 5.09 % Allowed : 15.48 % Favored : 79.43 % 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 aren not related in a simple way. whole: -0.59 (0.12), residues: 4633 helix: 0.28 (0.11), residues: 2205 sheet: -0.21 (0.19), residues: 674 loop : -1.22 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M1210 TYR 0.033 0.002 TYR M 699 PHE 0.025 0.002 PHE M1317 TRP 0.013 0.002 TRP M 818 HIS 0.007 0.001 HIS Y 299 Details of bonding type rmsd covalent geometry : bond 0.00523 (44998) covalent geometry : angle 0.70061 (62207) hydrogen bonds : bond 0.05521 ( 1999) hydrogen bonds : angle 4.56542 ( 5463) metal coordination : bond 0.01191 ( 8) metal coordination : angle 4.95344 ( 9) Misc. bond : bond 0.00194 ( 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 530 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 327 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ARG cc_start: 0.7040 (ttm170) cc_final: 0.6738 (mtt90) REVERT: B 59 GLU cc_start: 0.8167 (pp20) cc_final: 0.7844 (pp20) REVERT: C 71 THR cc_start: 0.9054 (m) cc_final: 0.8658 (p) REVERT: C 77 LYS cc_start: 0.8512 (mmmm) cc_final: 0.7798 (mptt) REVERT: D 30 THR cc_start: 0.6078 (t) cc_final: 0.5670 (m) REVERT: D 53 GLU cc_start: 0.7552 (tp30) cc_final: 0.7011 (mm-30) REVERT: D 92 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6876 (mtp85) REVERT: F 58 TYR cc_start: 0.6863 (t80) cc_final: 0.6389 (t80) REVERT: F 96 LYS cc_start: 0.7898 (tmmt) cc_final: 0.7241 (ptpp) REVERT: G 89 LYS cc_start: 0.6765 (mttt) cc_final: 0.6076 (ptmm) REVERT: H 49 LYS cc_start: 0.6718 (mmmt) cc_final: 0.5945 (mttp) REVERT: M 870 LEU cc_start: 0.7638 (mt) cc_final: 0.7207 (mt) REVERT: M 970 THR cc_start: 0.8187 (p) cc_final: 0.7663 (m) REVERT: M 980 MET cc_start: 0.7817 (mmt) cc_final: 0.7067 (ptp) REVERT: M 1339 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6375 (m-80) REVERT: R 283 PHE cc_start: 0.3377 (m-10) cc_final: 0.2925 (m-10) REVERT: S 170 GLU cc_start: 0.7227 (tp30) cc_final: 0.6890 (tp30) REVERT: S 220 MET cc_start: 0.6980 (ttp) cc_final: 0.6180 (tpt) REVERT: U 31 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7774 (mp) REVERT: U 81 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7809 (ttpp) REVERT: U 175 MET cc_start: 0.8595 (tpp) cc_final: 0.8233 (tpp) REVERT: U 301 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8492 (mp) REVERT: V 51 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.6263 (mp-120) REVERT: W 175 MET cc_start: 0.8531 (mmt) cc_final: 0.8162 (tpp) REVERT: X 85 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8317 (mtmm) REVERT: X 105 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7922 (tt) REVERT: X 312 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: X 377 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8069 (tmmt) REVERT: Y 220 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8075 (pmt170) REVERT: Y 310 ASN cc_start: 0.7936 (m-40) cc_final: 0.7584 (m110) REVERT: Y 313 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8816 (tt) outliers start: 203 outliers final: 136 residues processed: 502 average time/residue: 0.2753 time to fit residues: 227.7506 Evaluate side-chains 435 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 287 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 87 SER 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 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 98 LEU 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 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 805 LEU Chi-restraints excluded: chain M residue 811 HIS 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 965 MET 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 1117 ASP Chi-restraints excluded: chain M residue 1197 LEU 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 1340 ASP 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 53 SER Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 190 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 R residue 278 ASP Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 428 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 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 154 ASN Chi-restraints excluded: chain T residue 159 TYR 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 31 LEU 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 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 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 435 VAL Chi-restraints excluded: chain V residue 436 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 27 THR 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 350 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 420 VAL 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 92 ILE Chi-restraints excluded: chain X residue 105 LEU 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 300 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 332 ILE 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 240 SER Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 313 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 413 ARG 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: 0.9990 chunk 279 optimal weight: 0.7980 chunk 204 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 356 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 291 optimal weight: 0.7980 chunk 486 optimal weight: 1.9990 chunk 483 optimal weight: 0.8980 chunk 376 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1285 HIS ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1356 HIS U 223 GLN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.120231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.090728 restraints weight = 110151.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089998 restraints weight = 86607.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090350 restraints weight = 67899.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.090570 restraints weight = 57883.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.090612 restraints weight = 50250.142| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45008 Z= 0.127 Angle : 0.607 10.507 62216 Z= 0.312 Chirality : 0.040 0.239 7288 Planarity : 0.004 0.053 6836 Dihedral : 22.802 154.282 8688 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 3.83 % Allowed : 16.88 % Favored : 79.28 % 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 aren not related in a simple way. whole: -0.18 (0.12), residues: 4633 helix: 0.71 (0.11), residues: 2199 sheet: -0.17 (0.19), residues: 676 loop : -1.09 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 431 TYR 0.036 0.001 TYR H 86 PHE 0.028 0.001 PHE G 68 TRP 0.007 0.001 TRP M 818 HIS 0.016 0.001 HIS M 811 Details of bonding type rmsd covalent geometry : bond 0.00279 (44998) covalent geometry : angle 0.60529 (62207) hydrogen bonds : bond 0.04536 ( 1999) hydrogen bonds : angle 4.15385 ( 5463) metal coordination : bond 0.00983 ( 8) metal coordination : angle 4.06261 ( 9) Misc. bond : bond 0.00052 ( 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 487 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 334 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ARG cc_start: 0.7015 (ttm170) cc_final: 0.6808 (mtt90) REVERT: B 59 GLU cc_start: 0.8141 (pp20) cc_final: 0.7859 (pp20) REVERT: C 71 THR cc_start: 0.8960 (m) cc_final: 0.8571 (p) REVERT: C 77 LYS cc_start: 0.8421 (mmmm) cc_final: 0.7664 (mptt) REVERT: D 30 THR cc_start: 0.6206 (t) cc_final: 0.5826 (m) REVERT: D 53 GLU cc_start: 0.7495 (tp30) cc_final: 0.7051 (mm-30) REVERT: D 77 LYS cc_start: 0.6281 (mmtm) cc_final: 0.5845 (pttt) REVERT: D 92 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6887 (mtp85) REVERT: E 33 ARG cc_start: 0.7416 (tmm-80) cc_final: 0.7134 (ttp80) REVERT: E 76 LYS cc_start: 0.7839 (mttt) cc_final: 0.7580 (mmtp) REVERT: G 48 LEU cc_start: 0.8685 (tp) cc_final: 0.8393 (tp) REVERT: G 89 LYS cc_start: 0.6657 (mttt) cc_final: 0.6241 (ptmm) REVERT: H 49 LYS cc_start: 0.6571 (mmmt) cc_final: 0.5988 (mttp) REVERT: H 95 ARG cc_start: 0.7340 (mmm160) cc_final: 0.7098 (mtm180) REVERT: M 870 LEU cc_start: 0.7599 (mt) cc_final: 0.7291 (mt) REVERT: M 970 THR cc_start: 0.8103 (p) cc_final: 0.7517 (m) REVERT: M 980 MET cc_start: 0.7775 (mmt) cc_final: 0.7305 (mmt) REVERT: M 989 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7722 (mp) REVERT: M 1339 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: R 283 PHE cc_start: 0.3310 (m-10) cc_final: 0.2881 (m-10) REVERT: S 170 GLU cc_start: 0.7165 (tp30) cc_final: 0.6871 (tp30) REVERT: S 220 MET cc_start: 0.6847 (ttp) cc_final: 0.6112 (tpt) REVERT: T 70 MET cc_start: 0.7862 (mmm) cc_final: 0.7524 (mmm) REVERT: T 201 TYR cc_start: 0.7688 (t80) cc_final: 0.7442 (t80) REVERT: U 63 ASN cc_start: 0.8117 (t0) cc_final: 0.7856 (t0) REVERT: U 175 MET cc_start: 0.8517 (tpp) cc_final: 0.8249 (tpp) REVERT: U 283 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: X 85 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8067 (mtmm) REVERT: X 121 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8597 (tp) REVERT: X 125 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8259 (t80) REVERT: X 312 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: X 377 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7982 (tmmt) outliers start: 153 outliers final: 98 residues processed: 468 average time/residue: 0.2668 time to fit residues: 207.8457 Evaluate side-chains 407 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 300 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 71 ASP 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 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 805 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 965 MET Chi-restraints excluded: chain M residue 989 LEU 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 1117 ASP Chi-restraints excluded: chain M residue 1197 LEU 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 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 S residue 49 ILE Chi-restraints excluded: chain S residue 113 LEU 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 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 345 THR 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 141 VAL 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 121 LEU Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 228 GLU Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 302 GLU 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 435 VAL Chi-restraints excluded: chain V residue 436 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 353 ILE Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 92 ILE 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 281 THR 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 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 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 313 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 262 optimal weight: 0.6980 chunk 463 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN D 27 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1285 HIS M1352 GLN ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 HIS ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 23 HIS ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 443 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.113831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.084708 restraints weight = 111038.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.084684 restraints weight = 97213.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084602 restraints weight = 85383.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.084949 restraints weight = 71775.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085014 restraints weight = 62005.917| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.124 45008 Z= 0.371 Angle : 0.853 12.332 62216 Z= 0.442 Chirality : 0.049 0.204 7288 Planarity : 0.006 0.073 6836 Dihedral : 23.061 157.685 8679 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 5.04 % Allowed : 17.38 % Favored : 77.58 % 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 aren not related in a simple way. whole: -1.03 (0.12), residues: 4633 helix: 0.00 (0.11), residues: 2201 sheet: -0.64 (0.19), residues: 674 loop : -1.45 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 348 TYR 0.039 0.003 TYR V 462 PHE 0.036 0.003 PHE M1317 TRP 0.012 0.002 TRP R 199 HIS 0.011 0.002 HIS M1225 Details of bonding type rmsd covalent geometry : bond 0.00883 (44998) covalent geometry : angle 0.85049 (62207) hydrogen bonds : bond 0.06720 ( 1999) hydrogen bonds : angle 5.00366 ( 5463) metal coordination : bond 0.01247 ( 8) metal coordination : angle 5.50908 ( 9) Misc. bond : bond 0.00288 ( 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 494 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 293 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6853 (t80) cc_final: 0.6648 (t80) REVERT: B 59 GLU cc_start: 0.8260 (pp20) cc_final: 0.7985 (pp20) REVERT: C 27 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8325 (mm-40) REVERT: C 71 THR cc_start: 0.9082 (m) cc_final: 0.8879 (p) REVERT: C 77 LYS cc_start: 0.8410 (mmmm) cc_final: 0.7738 (mptt) REVERT: D 30 THR cc_start: 0.6357 (t) cc_final: 0.5927 (m) REVERT: D 53 GLU cc_start: 0.7712 (tp30) cc_final: 0.7242 (mm-30) REVERT: D 92 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7389 (ptm160) REVERT: F 37 ARG cc_start: 0.8057 (mmm160) cc_final: 0.6616 (mtt180) REVERT: H 49 LYS cc_start: 0.6753 (mmmt) cc_final: 0.5894 (mttp) REVERT: M 970 THR cc_start: 0.8215 (p) cc_final: 0.7637 (m) REVERT: M 1069 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7584 (ptpp) REVERT: M 1339 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: R 279 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.5460 (t80) REVERT: S 220 MET cc_start: 0.7043 (ttp) cc_final: 0.6315 (tpt) REVERT: T 278 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8593 (p) REVERT: U 283 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: V 51 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6430 (mp-120) REVERT: V 88 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8996 (mp) REVERT: V 366 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7056 (mtp85) REVERT: X 85 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8292 (mtmm) REVERT: X 125 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7644 (t80) REVERT: X 312 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: X 377 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8168 (tmmt) outliers start: 201 outliers final: 139 residues processed: 468 average time/residue: 0.2657 time to fit residues: 207.5716 Evaluate side-chains 421 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 269 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 89 ILE 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 82 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 71 ASP 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 109 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 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 965 MET 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 1069 LYS 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 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 53 SER 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 201 ILE 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 255 VAL 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 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 179 TYR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 263 ILE 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 131 LEU Chi-restraints excluded: chain T residue 135 GLU Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 159 TYR Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 345 THR Chi-restraints excluded: chain T residue 353 VAL Chi-restraints excluded: chain T residue 455 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 31 LEU Chi-restraints excluded: chain U residue 141 VAL 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 V residue 51 GLN Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 163 ILE 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 254 VAL 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 366 ARG Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 436 VAL Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 27 THR 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 148 SER 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 222 VAL Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 92 ILE 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 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 281 THR Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 373 LEU 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 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 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 370 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: 0.3980 chunk 214 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 413 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 365 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1285 HIS ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 272 GLN Y 223 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.118176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.088660 restraints weight = 109059.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088785 restraints weight = 93862.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.088825 restraints weight = 70362.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089050 restraints weight = 64091.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.089136 restraints weight = 56314.419| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45008 Z= 0.135 Angle : 0.632 11.505 62216 Z= 0.326 Chirality : 0.041 0.195 7288 Planarity : 0.004 0.055 6836 Dihedral : 22.872 156.288 8670 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 3.31 % Allowed : 19.11 % Favored : 77.58 % 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 aren not related in a simple way. whole: -0.42 (0.12), residues: 4633 helix: 0.59 (0.11), residues: 2197 sheet: -0.44 (0.19), residues: 679 loop : -1.24 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 49 TYR 0.037 0.001 TYR M 699 PHE 0.035 0.001 PHE G 68 TRP 0.008 0.001 TRP M 706 HIS 0.008 0.001 HIS T 250 Details of bonding type rmsd covalent geometry : bond 0.00298 (44998) covalent geometry : angle 0.63019 (62207) hydrogen bonds : bond 0.04804 ( 1999) hydrogen bonds : angle 4.28093 ( 5463) metal coordination : bond 0.01421 ( 8) metal coordination : angle 4.09570 ( 9) Misc. bond : bond 0.00080 ( 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 441 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 309 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7581 (tp30) cc_final: 0.7263 (mp0) REVERT: B 59 GLU cc_start: 0.8193 (pp20) cc_final: 0.7926 (pp20) REVERT: C 71 THR cc_start: 0.9001 (m) cc_final: 0.8669 (p) REVERT: C 77 LYS cc_start: 0.8393 (mmmm) cc_final: 0.7668 (mptt) REVERT: D 30 THR cc_start: 0.6109 (t) cc_final: 0.5706 (m) REVERT: D 53 GLU cc_start: 0.7637 (tp30) cc_final: 0.7095 (mm-30) REVERT: D 77 LYS cc_start: 0.6311 (mmtm) cc_final: 0.5852 (pttt) REVERT: D 92 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7412 (ptm160) REVERT: F 37 ARG cc_start: 0.8090 (mmm160) cc_final: 0.6761 (ttm110) REVERT: F 63 ILE cc_start: 0.7505 (mm) cc_final: 0.7199 (tp) REVERT: G 89 LYS cc_start: 0.6855 (mttp) cc_final: 0.6367 (ptmt) REVERT: H 49 LYS cc_start: 0.6530 (mmmt) cc_final: 0.5876 (mttp) REVERT: H 95 ARG cc_start: 0.7427 (mmm160) cc_final: 0.7071 (mtt180) REVERT: M 825 GLU cc_start: 0.8648 (mp0) cc_final: 0.8415 (mp0) REVERT: M 870 LEU cc_start: 0.7599 (mt) cc_final: 0.7165 (mt) REVERT: M 980 MET cc_start: 0.7844 (mmt) cc_final: 0.7292 (mmt) REVERT: M 1280 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7592 (tm-30) REVERT: M 1339 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6369 (m-80) REVERT: R 279 PHE cc_start: 0.6445 (OUTLIER) cc_final: 0.5826 (t80) REVERT: R 283 PHE cc_start: 0.3475 (m-10) cc_final: 0.2697 (m-10) REVERT: S 170 GLU cc_start: 0.7156 (tp30) cc_final: 0.6759 (tp30) REVERT: S 220 MET cc_start: 0.6909 (ttp) cc_final: 0.6100 (tpt) REVERT: T 70 MET cc_start: 0.7736 (mmm) cc_final: 0.7417 (mmm) REVERT: T 278 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8389 (p) REVERT: U 283 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: W 109 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8725 (tt) REVERT: X 125 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8106 (t80) REVERT: X 312 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: X 377 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7936 (tmmt) REVERT: Y 310 ASN cc_start: 0.7931 (m-40) cc_final: 0.7523 (m110) outliers start: 132 outliers final: 98 residues processed: 427 average time/residue: 0.2600 time to fit residues: 186.6447 Evaluate side-chains 401 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 294 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE 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 G residue 71 ASP Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 805 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 965 MET 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 1117 ASP Chi-restraints excluded: chain M residue 1199 LEU 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 70 GLU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 190 VAL 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 316 THR Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 116 VAL 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 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 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 141 VAL Chi-restraints excluded: chain U residue 257 LEU 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 121 LEU Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 228 GLU Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 304 ILE 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 435 VAL Chi-restraints excluded: chain V residue 436 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 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 302 ASP Chi-restraints excluded: chain W residue 341 HIS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 150 GLU 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 281 THR Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 395 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 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 55 optimal weight: 5.9990 chunk 192 optimal weight: 0.0020 chunk 298 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 487 optimal weight: 0.9980 chunk 485 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 339 optimal weight: 1.9990 chunk 440 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1285 HIS ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 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 = 0.3968 r_free = 0.3968 target = 0.117327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088522 restraints weight = 110018.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.087548 restraints weight = 103063.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087800 restraints weight = 82945.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088198 restraints weight = 67765.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088255 restraints weight = 58933.187| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4739 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= 0.162 Angle : 0.639 11.890 62216 Z= 0.329 Chirality : 0.041 0.198 7288 Planarity : 0.004 0.053 6836 Dihedral : 22.787 157.100 8664 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 3.51 % Allowed : 19.11 % Favored : 77.38 % 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 aren not related in a simple way. whole: -0.38 (0.12), residues: 4633 helix: 0.62 (0.11), residues: 2223 sheet: -0.44 (0.19), residues: 667 loop : -1.24 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.028 0.001 TYR D 88 PHE 0.024 0.002 PHE R 120 TRP 0.008 0.001 TRP R 199 HIS 0.006 0.001 HIS T 250 Details of bonding type rmsd covalent geometry : bond 0.00376 (44998) covalent geometry : angle 0.63723 (62207) hydrogen bonds : bond 0.04874 ( 1999) hydrogen bonds : angle 4.26338 ( 5463) metal coordination : bond 0.01074 ( 8) metal coordination : angle 3.87169 ( 9) Misc. bond : bond 0.00110 ( 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 436 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 296 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7572 (tp30) cc_final: 0.7255 (mp0) REVERT: B 59 GLU cc_start: 0.8202 (pp20) cc_final: 0.7911 (pp20) REVERT: C 71 THR cc_start: 0.9008 (m) cc_final: 0.8757 (p) REVERT: C 77 LYS cc_start: 0.8405 (mmmm) cc_final: 0.7656 (mptt) REVERT: D 30 THR cc_start: 0.6217 (t) cc_final: 0.5883 (m) REVERT: D 53 GLU cc_start: 0.7717 (tp30) cc_final: 0.7118 (mm-30) REVERT: D 77 LYS cc_start: 0.6221 (mmtm) cc_final: 0.5754 (pttt) REVERT: D 92 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7362 (ptm160) REVERT: F 37 ARG cc_start: 0.8118 (mmm160) cc_final: 0.6507 (mtt180) REVERT: G 48 LEU cc_start: 0.8688 (tp) cc_final: 0.8407 (tp) REVERT: H 49 LYS cc_start: 0.6691 (mmmt) cc_final: 0.5971 (mttp) REVERT: M 825 GLU cc_start: 0.8777 (mp0) cc_final: 0.8433 (mp0) REVERT: M 870 LEU cc_start: 0.7481 (mt) cc_final: 0.7143 (mt) REVERT: M 989 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7853 (mp) REVERT: M 1280 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7615 (tm-30) REVERT: M 1339 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: R 279 PHE cc_start: 0.6477 (OUTLIER) cc_final: 0.6006 (t80) REVERT: R 283 PHE cc_start: 0.3665 (m-80) cc_final: 0.2741 (m-10) REVERT: S 170 GLU cc_start: 0.7376 (tp30) cc_final: 0.6991 (tp30) REVERT: S 220 MET cc_start: 0.6940 (ttp) cc_final: 0.6071 (tpt) REVERT: T 70 MET cc_start: 0.7780 (mmm) cc_final: 0.7444 (mmm) REVERT: T 278 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8450 (p) REVERT: U 283 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: V 386 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7736 (mtt-85) REVERT: W 109 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8762 (tt) REVERT: X 125 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7880 (t80) REVERT: X 312 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: Y 310 ASN cc_start: 0.8063 (m-40) cc_final: 0.7612 (m110) outliers start: 140 outliers final: 107 residues processed: 418 average time/residue: 0.2616 time to fit residues: 183.8510 Evaluate side-chains 399 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 282 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE 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 F residue 50 VAL Chi-restraints excluded: chain G residue 71 ASP 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 109 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 805 LEU Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 965 MET Chi-restraints excluded: chain M residue 989 LEU 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 1117 ASP Chi-restraints excluded: chain M residue 1199 LEU 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 149 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 201 ILE 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 316 THR 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 192 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 263 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 125 PHE Chi-restraints excluded: chain T residue 135 GLU 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 141 VAL Chi-restraints excluded: chain U residue 244 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 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 228 GLU Chi-restraints excluded: chain V residue 286 GLN 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 386 ARG 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 V residue 436 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 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 222 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 302 ASP Chi-restraints excluded: chain W residue 341 HIS Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 281 THR Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 256 optimal weight: 6.9990 chunk 332 optimal weight: 4.9990 chunk 346 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 196 optimal weight: 0.0980 chunk 86 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 328 optimal weight: 3.9990 chunk 477 optimal weight: 0.9980 chunk 443 optimal weight: 0.5980 chunk 388 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 811 HIS ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 205 ASN ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.117575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088700 restraints weight = 109230.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088841 restraints weight = 96964.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.088769 restraints weight = 81743.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.089139 restraints weight = 70468.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.089178 restraints weight = 60979.376| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 45008 Z= 0.154 Angle : 0.631 11.654 62216 Z= 0.325 Chirality : 0.040 0.192 7288 Planarity : 0.004 0.053 6836 Dihedral : 22.748 157.369 8662 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 3.48 % Allowed : 19.39 % Favored : 77.13 % 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 aren not related in a simple way. whole: -0.31 (0.12), residues: 4633 helix: 0.71 (0.11), residues: 2223 sheet: -0.44 (0.20), residues: 672 loop : -1.24 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 49 TYR 0.027 0.001 TYR D 88 PHE 0.026 0.002 PHE W 206 TRP 0.008 0.001 TRP M 706 HIS 0.006 0.001 HIS T 250 Details of bonding type rmsd covalent geometry : bond 0.00357 (44998) covalent geometry : angle 0.62996 (62207) hydrogen bonds : bond 0.04719 ( 1999) hydrogen bonds : angle 4.20121 ( 5463) metal coordination : bond 0.01091 ( 8) metal coordination : angle 3.68020 ( 9) Misc. bond : bond 0.00100 ( 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 435 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 296 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6553 (t80) cc_final: 0.6250 (t80) REVERT: B 59 GLU cc_start: 0.8225 (pp20) cc_final: 0.7966 (pp20) REVERT: B 115 LYS cc_start: 0.7586 (mmmt) cc_final: 0.6393 (mppt) REVERT: C 71 THR cc_start: 0.9051 (m) cc_final: 0.8629 (p) REVERT: C 77 LYS cc_start: 0.8362 (mmmm) cc_final: 0.7670 (mptt) REVERT: D 30 THR cc_start: 0.6251 (t) cc_final: 0.5864 (m) REVERT: D 53 GLU cc_start: 0.7771 (tp30) cc_final: 0.7233 (mm-30) REVERT: D 77 LYS cc_start: 0.6351 (mmtm) cc_final: 0.5882 (pttt) REVERT: D 92 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7401 (ptm160) REVERT: F 37 ARG cc_start: 0.7980 (mmm160) cc_final: 0.6438 (mtt180) REVERT: G 48 LEU cc_start: 0.8588 (tp) cc_final: 0.8271 (tp) REVERT: H 49 LYS cc_start: 0.6586 (mmmt) cc_final: 0.5897 (mttp) REVERT: M 825 GLU cc_start: 0.8630 (mp0) cc_final: 0.8348 (mp0) REVERT: M 870 LEU cc_start: 0.7373 (mt) cc_final: 0.6942 (mt) REVERT: M 989 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7846 (mp) REVERT: M 1278 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8514 (mt) REVERT: M 1280 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7601 (tm-30) REVERT: M 1339 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: R 147 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6064 (tpt) REVERT: R 279 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5903 (t80) REVERT: R 283 PHE cc_start: 0.3571 (m-80) cc_final: 0.2605 (m-10) REVERT: S 99 ASP cc_start: 0.6320 (p0) cc_final: 0.6007 (m-30) REVERT: S 170 GLU cc_start: 0.7164 (tp30) cc_final: 0.6770 (tp30) REVERT: S 220 MET cc_start: 0.6945 (ttp) cc_final: 0.6183 (tpt) REVERT: T 70 MET cc_start: 0.7753 (mmm) cc_final: 0.7423 (mmm) REVERT: T 278 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8479 (p) REVERT: U 283 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: W 109 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8792 (tt) REVERT: X 125 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7918 (t80) REVERT: X 312 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: Y 310 ASN cc_start: 0.8038 (m-40) cc_final: 0.7578 (m110) outliers start: 139 outliers final: 112 residues processed: 417 average time/residue: 0.2594 time to fit residues: 182.5263 Evaluate side-chains 406 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 283 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE 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 F residue 50 VAL Chi-restraints excluded: chain G residue 71 ASP 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 109 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 805 LEU Chi-restraints excluded: chain M residue 811 HIS Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 965 MET Chi-restraints excluded: chain M residue 989 LEU 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 1117 ASP Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1278 LEU 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 53 SER Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 147 MET Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 190 VAL 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 316 THR 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 192 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 263 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 125 PHE Chi-restraints excluded: chain T residue 135 GLU Chi-restraints excluded: chain T residue 237 VAL 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 141 VAL 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 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 228 GLU Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 286 GLN 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 V residue 436 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 148 SER 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 222 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 302 ASP Chi-restraints excluded: chain W residue 341 HIS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 281 THR Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 393 LEU Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 455 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 351 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 440 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 250 optimal weight: 0.5980 chunk 471 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 811 HIS M 827 HIS M1285 HIS ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.087880 restraints weight = 109575.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088042 restraints weight = 96024.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.087985 restraints weight = 79571.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088220 restraints weight = 70517.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088373 restraints weight = 60978.753| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 45008 Z= 0.173 Angle : 0.653 12.751 62216 Z= 0.336 Chirality : 0.041 0.190 7288 Planarity : 0.004 0.051 6836 Dihedral : 22.748 157.853 8662 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 3.26 % Allowed : 19.71 % Favored : 77.03 % 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 aren not related in a simple way. whole: -0.36 (0.12), residues: 4633 helix: 0.70 (0.11), residues: 2216 sheet: -0.48 (0.20), residues: 665 loop : -1.28 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.028 0.002 TYR D 88 PHE 0.025 0.002 PHE W 206 TRP 0.008 0.001 TRP M 706 HIS 0.013 0.001 HIS M 811 Details of bonding type rmsd covalent geometry : bond 0.00406 (44998) covalent geometry : angle 0.65165 (62207) hydrogen bonds : bond 0.04879 ( 1999) hydrogen bonds : angle 4.25889 ( 5463) metal coordination : bond 0.01156 ( 8) metal coordination : angle 3.85809 ( 9) Misc. bond : bond 0.00111 ( 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 425 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 295 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6583 (t80) cc_final: 0.6340 (t80) REVERT: B 59 GLU cc_start: 0.8233 (pp20) cc_final: 0.7965 (pp20) REVERT: B 115 LYS cc_start: 0.7620 (mmmt) cc_final: 0.6455 (mppt) REVERT: C 71 THR cc_start: 0.8976 (m) cc_final: 0.8563 (p) REVERT: C 77 LYS cc_start: 0.8326 (mmmm) cc_final: 0.7610 (mptt) REVERT: D 30 THR cc_start: 0.6285 (t) cc_final: 0.5880 (m) REVERT: D 53 GLU cc_start: 0.7788 (tp30) cc_final: 0.7242 (mm-30) REVERT: D 77 LYS cc_start: 0.6370 (mmtm) cc_final: 0.5889 (pttt) REVERT: D 92 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7424 (ptm160) REVERT: E 57 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7066 (tm-30) REVERT: F 37 ARG cc_start: 0.7995 (mmm160) cc_final: 0.6448 (mtt180) REVERT: H 49 LYS cc_start: 0.6717 (mmmt) cc_final: 0.5976 (mttp) REVERT: M 825 GLU cc_start: 0.8654 (mp0) cc_final: 0.8428 (mp0) REVERT: M 870 LEU cc_start: 0.7219 (mt) cc_final: 0.6958 (mt) REVERT: M 989 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7807 (mp) REVERT: M 1278 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8482 (mt) REVERT: M 1280 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7618 (tm-30) REVERT: M 1339 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: R 147 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.5896 (tpt) REVERT: R 279 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5782 (t80) REVERT: R 283 PHE cc_start: 0.3460 (m-80) cc_final: 0.2647 (m-10) REVERT: S 96 LEU cc_start: 0.8378 (mt) cc_final: 0.8170 (tt) REVERT: S 99 ASP cc_start: 0.6391 (p0) cc_final: 0.6066 (m-30) REVERT: S 170 GLU cc_start: 0.7211 (tp30) cc_final: 0.6817 (tp30) REVERT: S 220 MET cc_start: 0.6962 (ttp) cc_final: 0.6178 (tpt) REVERT: T 70 MET cc_start: 0.7782 (mmm) cc_final: 0.7415 (mmm) REVERT: T 278 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8515 (p) REVERT: U 283 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: V 315 MET cc_start: 0.7673 (mmm) cc_final: 0.7157 (mmm) REVERT: W 109 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8756 (tt) REVERT: X 312 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: Y 310 ASN cc_start: 0.8057 (m-40) cc_final: 0.7602 (m110) outliers start: 130 outliers final: 115 residues processed: 407 average time/residue: 0.2628 time to fit residues: 179.8222 Evaluate side-chains 410 residues out of total 4069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 285 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE 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 F residue 50 VAL Chi-restraints excluded: chain G residue 71 ASP 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 109 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 805 LEU Chi-restraints excluded: chain M residue 811 HIS Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 965 MET Chi-restraints excluded: chain M residue 989 LEU 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 1117 ASP Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1278 LEU 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 53 SER Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 147 MET Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 190 VAL 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 316 THR 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 192 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 263 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 125 PHE Chi-restraints excluded: chain T residue 135 GLU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 269 MET 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 141 VAL 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 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 228 GLU Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 286 GLN 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 V residue 436 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 148 SER 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 222 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 302 ASP Chi-restraints excluded: chain W residue 341 HIS Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 281 THR Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 393 LEU Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 240 SER Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 264 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 435 optimal weight: 1.9990 chunk 367 optimal weight: 0.9980 chunk 439 optimal weight: 0.6980 chunk 316 optimal weight: 0.6980 chunk 236 optimal weight: 0.9990 chunk 392 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 811 HIS M1285 HIS ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 47 GLN U 155 GLN ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.118624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.089690 restraints weight = 109944.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.088918 restraints weight = 101663.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.089138 restraints weight = 80547.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.089519 restraints weight = 66439.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.089581 restraints weight = 57831.458| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45008 Z= 0.131 Angle : 0.624 12.573 62216 Z= 0.320 Chirality : 0.040 0.190 7288 Planarity : 0.004 0.052 6836 Dihedral : 22.683 157.639 8662 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.58 % Favored : 95.40 % Rotamer: Outliers : 3.21 % Allowed : 19.84 % Favored : 76.95 % 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 aren not related in a simple way. whole: -0.18 (0.12), residues: 4633 helix: 0.83 (0.11), residues: 2224 sheet: -0.41 (0.20), residues: 679 loop : -1.18 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 49 TYR 0.026 0.001 TYR D 88 PHE 0.013 0.001 PHE M 813 TRP 0.009 0.001 TRP M 706 HIS 0.014 0.001 HIS M 811 Details of bonding type rmsd covalent geometry : bond 0.00293 (44998) covalent geometry : angle 0.62239 (62207) hydrogen bonds : bond 0.04524 ( 1999) hydrogen bonds : angle 4.09850 ( 5463) metal coordination : bond 0.00970 ( 8) metal coordination : angle 3.47518 ( 9) Misc. bond : bond 0.00062 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7406.18 seconds wall clock time: 129 minutes 20.14 seconds (7760.14 seconds total)