Starting phenix.real_space_refine on Fri Oct 11 09:40:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/10_2024/8x15_37984_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/10_2024/8x15_37984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/10_2024/8x15_37984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/10_2024/8x15_37984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/10_2024/8x15_37984_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x15_37984/10_2024/8x15_37984_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 291 5.49 5 S 252 5.16 5 C 34081 2.51 5 N 9849 2.21 5 O 11015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 486 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 55488 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "H" 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: "I" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6519 Classifications: {'peptide': 792} Link IDs: {'PTRANS': 48, 'TRANS': 743} Chain breaks: 4 Chain: "J" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1316 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 13, 'TRANS': 144} Chain breaks: 1 Chain: "K" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3209 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain: "L" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain breaks: 1 Chain: "M" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3213 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3185 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 10, 'TRANS': 400} Chain breaks: 2 Chain: "O" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3287 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3368 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 422} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3293 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 10, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "T" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3146 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 1 Chain: "U" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2802 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "V" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1617 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain breaks: 1 Chain: "W" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1542 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 178} Chain: "X" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2829 Classifications: {'DNA': 137} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 136} Chain: "Y" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2785 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.23, per 1000 atoms: 0.42 Number of scatterers: 55488 At special positions: 0 Unit cell: (204.102, 184.092, 229.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 252 16.00 P 291 15.00 O 11015 8.00 N 9849 7.00 C 34081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 54662 O4' DT Y -29 .*. O " rejected from bonding due to valence issues. Atom "ATOM 54763 O4' DG Y -24 .*. O " rejected from bonding due to valence issues. Atom "HETATM55313 O3A ADP N 501 .*. O " rejected from bonding due to valence issues. Atom "ATOM 53097 O5' DG Y-106 .*. O " rejected from bonding due to valence issues. Atom "HETATM55316 O5' ADP N 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.27 Conformation dependent library (CDL) restraints added in 5.0 seconds 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11734 Finding SS restraints... Secondary structure from input PDB file: 276 helices and 61 sheets defined 50.9% alpha, 10.7% beta 111 base pairs and 217 stacking pairs defined. Time for finding SS restraints: 15.71 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 27 through 38 Processing helix chain 'A' and resid 46 through 75 removed outlier: 4.044A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.528A pdb=" N ASN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.691A pdb=" N LEU A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 removed outlier: 3.539A pdb=" N LYS B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 81 Processing helix chain 'B' and resid 87 through 99 Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.690A pdb=" N ALA B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 55 Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.622A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 removed outlier: 3.596A pdb=" N LEU C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.681A pdb=" N ILE C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 48 through 76 removed outlier: 4.493A pdb=" N GLU D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 76 " --> pdb=" O TYR D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.584A pdb=" N VAL D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 22 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 45 through 71 removed outlier: 4.479A pdb=" N VAL E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'F' and resid 34 through 46 Processing helix chain 'F' and resid 52 through 81 Processing helix chain 'F' and resid 87 through 97 Processing helix chain 'F' and resid 101 through 120 Processing helix chain 'G' and resid 44 through 55 removed outlier: 3.756A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 77 removed outlier: 3.577A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 removed outlier: 3.562A pdb=" N MET G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.515A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.936A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'I' and resid 94 through 117 Processing helix chain 'I' and resid 136 through 249 removed outlier: 4.198A pdb=" N LEU I 140 " --> pdb=" O HIS I 136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA I 149 " --> pdb=" O GLN I 145 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP I 150 " --> pdb=" O TRP I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 635 Processing helix chain 'I' and resid 648 through 663 Processing helix chain 'I' and resid 675 through 677 No H-bonds generated for 'chain 'I' and resid 675 through 677' Processing helix chain 'I' and resid 678 through 690 Processing helix chain 'I' and resid 701 through 710 Processing helix chain 'I' and resid 724 through 731 Processing helix chain 'I' and resid 731 through 737 Processing helix chain 'I' and resid 748 through 752 removed outlier: 3.728A pdb=" N LYS I 752 " --> pdb=" O GLN I 749 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 764 Processing helix chain 'I' and resid 781 through 792 Processing helix chain 'I' and resid 866 through 875 Processing helix chain 'I' and resid 875 through 884 Processing helix chain 'I' and resid 886 through 901 Processing helix chain 'I' and resid 903 through 907 Processing helix chain 'I' and resid 936 through 940 removed outlier: 4.176A pdb=" N ARG I 940 " --> pdb=" O PRO I 937 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 947 Processing helix chain 'I' and resid 956 through 962 Processing helix chain 'I' and resid 963 through 968 Processing helix chain 'I' and resid 970 through 978 removed outlier: 3.850A pdb=" N ALA I 978 " --> pdb=" O LEU I 974 " (cutoff:3.500A) Processing helix chain 'I' and resid 1886 through 1911 Processing helix chain 'I' and resid 1919 through 1927 Processing helix chain 'I' and resid 1945 through 1950 removed outlier: 4.151A pdb=" N TRP I1949 " --> pdb=" O HIS I1945 " (cutoff:3.500A) Processing helix chain 'I' and resid 1952 through 1957 Processing helix chain 'I' and resid 1961 through 1977 removed outlier: 4.781A pdb=" N GLU I1971 " --> pdb=" O ASP I1967 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE I1972 " --> pdb=" O GLN I1968 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG I1975 " --> pdb=" O GLU I1971 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE I1977 " --> pdb=" O ILE I1973 " (cutoff:3.500A) Processing helix chain 'I' and resid 1998 through 2014 removed outlier: 4.121A pdb=" N ARG I2002 " --> pdb=" O TRP I1998 " (cutoff:3.500A) Processing helix chain 'I' and resid 2015 through 2020 removed outlier: 3.700A pdb=" N ARG I2019 " --> pdb=" O PRO I2016 " (cutoff:3.500A) Proline residue: I2020 - end of helix Processing helix chain 'I' and resid 2021 through 2030 Processing helix chain 'I' and resid 2042 through 2057 removed outlier: 3.851A pdb=" N ALA I2057 " --> pdb=" O ARG I2053 " (cutoff:3.500A) Processing helix chain 'I' and resid 2068 through 2080 Processing helix chain 'I' and resid 2094 through 2105 Processing helix chain 'I' and resid 2144 through 2153 removed outlier: 3.703A pdb=" N ALA I2148 " --> pdb=" O MET I2144 " (cutoff:3.500A) Processing helix chain 'I' and resid 2172 through 2190 Processing helix chain 'J' and resid 138 through 157 removed outlier: 4.160A pdb=" N THR J 144 " --> pdb=" O HIS J 140 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN J 152 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY J 153 " --> pdb=" O GLN J 149 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 199 removed outlier: 4.135A pdb=" N LEU J 182 " --> pdb=" O ILE J 178 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN J 183 " --> pdb=" O THR J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 276 removed outlier: 4.332A pdb=" N GLU J 275 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 330 removed outlier: 3.521A pdb=" N ALA J 322 " --> pdb=" O ILE J 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 48 removed outlier: 4.051A pdb=" N ILE K 45 " --> pdb=" O ALA K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.963A pdb=" N GLN K 71 " --> pdb=" O ASN K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 116 Processing helix chain 'K' and resid 126 through 139 Processing helix chain 'K' and resid 176 through 193 Processing helix chain 'K' and resid 199 through 210 removed outlier: 3.764A pdb=" N GLU K 207 " --> pdb=" O ASN K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 225 Processing helix chain 'K' and resid 271 through 277 removed outlier: 4.074A pdb=" N PHE K 275 " --> pdb=" O ALA K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 281 Processing helix chain 'K' and resid 294 through 301 Processing helix chain 'K' and resid 308 through 316 removed outlier: 3.970A pdb=" N HIS K 312 " --> pdb=" O GLU K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 323 through 326 removed outlier: 4.085A pdb=" N PHE K 326 " --> pdb=" O ASN K 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 323 through 326' Processing helix chain 'K' and resid 328 through 341 Processing helix chain 'K' and resid 357 through 367 Processing helix chain 'K' and resid 371 through 376 Processing helix chain 'K' and resid 379 through 386 Processing helix chain 'K' and resid 387 through 393 Processing helix chain 'L' and resid 20 through 37 Processing helix chain 'L' and resid 84 through 93 Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 137 through 148 Processing helix chain 'M' and resid 42 through 59 removed outlier: 3.657A pdb=" N LEU M 55 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 88 Processing helix chain 'M' and resid 99 through 102 Processing helix chain 'M' and resid 107 through 120 removed outlier: 3.963A pdb=" N ILE M 120 " --> pdb=" O PHE M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 184 removed outlier: 3.517A pdb=" N PHE M 177 " --> pdb=" O ASP M 173 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU M 178 " --> pdb=" O PRO M 174 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER M 179 " --> pdb=" O SER M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 249 removed outlier: 3.919A pdb=" N ASP M 244 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG M 249 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 262 removed outlier: 3.549A pdb=" N GLN M 262 " --> pdb=" O MET M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 290 Processing helix chain 'M' and resid 303 through 307 Processing helix chain 'M' and resid 308 through 319 Processing helix chain 'M' and resid 347 through 350 Processing helix chain 'M' and resid 351 through 356 Processing helix chain 'M' and resid 367 through 383 Processing helix chain 'M' and resid 387 through 401 Processing helix chain 'M' and resid 402 through 409 Processing helix chain 'M' and resid 409 through 421 removed outlier: 4.012A pdb=" N ALA M 413 " --> pdb=" O LEU M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 437 removed outlier: 3.981A pdb=" N VAL M 430 " --> pdb=" O GLU M 426 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU M 431 " --> pdb=" O LYS M 427 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU M 432 " --> pdb=" O GLU M 428 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU M 435 " --> pdb=" O GLU M 431 " (cutoff:3.500A) Processing helix chain 'M' and resid 441 through 448 Processing helix chain 'N' and resid 49 through 66 removed outlier: 3.508A pdb=" N VAL N 58 " --> pdb=" O ARG N 54 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 95 removed outlier: 3.776A pdb=" N ALA N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 126 Processing helix chain 'N' and resid 175 through 184 Processing helix chain 'N' and resid 244 through 253 removed outlier: 4.404A pdb=" N ARG N 253 " --> pdb=" O VAL N 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 284 Processing helix chain 'N' and resid 300 through 304 Processing helix chain 'N' and resid 305 through 316 removed outlier: 3.855A pdb=" N ARG N 314 " --> pdb=" O SER N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 352 Processing helix chain 'N' and resid 363 through 378 Processing helix chain 'N' and resid 383 through 397 removed outlier: 3.638A pdb=" N THR N 397 " --> pdb=" O ILE N 393 " (cutoff:3.500A) Processing helix chain 'N' and resid 398 through 414 removed outlier: 4.113A pdb=" N ALA N 402 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR N 407 " --> pdb=" O ILE N 403 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA N 408 " --> pdb=" O GLN N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 422 through 433 Processing helix chain 'N' and resid 435 through 441 removed outlier: 3.656A pdb=" N GLN N 441 " --> pdb=" O SER N 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 59 removed outlier: 3.669A pdb=" N VAL O 51 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS O 59 " --> pdb=" O LEU O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 88 Processing helix chain 'O' and resid 99 through 102 Processing helix chain 'O' and resid 107 through 119 removed outlier: 3.500A pdb=" N LEU O 112 " --> pdb=" O LYS O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 184 Processing helix chain 'O' and resid 208 through 213 removed outlier: 4.286A pdb=" N THR O 211 " --> pdb=" O THR O 208 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE O 213 " --> pdb=" O ALA O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 240 through 249 Processing helix chain 'O' and resid 256 through 262 Processing helix chain 'O' and resid 271 through 276 Processing helix chain 'O' and resid 277 through 288 Processing helix chain 'O' and resid 303 through 307 removed outlier: 4.181A pdb=" N MET O 306 " --> pdb=" O GLU O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 320 removed outlier: 3.601A pdb=" N HIS O 316 " --> pdb=" O PHE O 312 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 356 Processing helix chain 'O' and resid 367 through 382 Processing helix chain 'O' and resid 387 through 401 Processing helix chain 'O' and resid 402 through 409 Processing helix chain 'O' and resid 409 through 421 removed outlier: 3.524A pdb=" N ALA O 413 " --> pdb=" O LEU O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 426 through 437 Processing helix chain 'O' and resid 439 through 450 Processing helix chain 'O' and resid 451 through 454 removed outlier: 3.629A pdb=" N TYR O 454 " --> pdb=" O GLN O 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 451 through 454' Processing helix chain 'P' and resid 49 through 66 Processing helix chain 'P' and resid 82 through 95 Processing helix chain 'P' and resid 106 through 109 removed outlier: 3.755A pdb=" N PHE P 109 " --> pdb=" O SER P 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 106 through 109' Processing helix chain 'P' and resid 114 through 125 Processing helix chain 'P' and resid 175 through 186 Processing helix chain 'P' and resid 210 through 212 No H-bonds generated for 'chain 'P' and resid 210 through 212' Processing helix chain 'P' and resid 244 through 253 removed outlier: 4.419A pdb=" N ARG P 253 " --> pdb=" O VAL P 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 262 Processing helix chain 'P' and resid 270 through 287 removed outlier: 3.658A pdb=" N GLU P 274 " --> pdb=" O SER P 270 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 304 Processing helix chain 'P' and resid 305 through 316 removed outlier: 4.114A pdb=" N ARG P 314 " --> pdb=" O SER P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 346 Processing helix chain 'P' and resid 347 through 352 Processing helix chain 'P' and resid 363 through 378 Processing helix chain 'P' and resid 383 through 397 Processing helix chain 'P' and resid 398 through 416 removed outlier: 3.698A pdb=" N ILE P 406 " --> pdb=" O ALA P 402 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR P 407 " --> pdb=" O ILE P 403 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA P 408 " --> pdb=" O GLN P 404 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL P 412 " --> pdb=" O ALA P 408 " (cutoff:3.500A) Processing helix chain 'P' and resid 422 through 433 removed outlier: 3.582A pdb=" N ILE P 426 " --> pdb=" O GLN P 422 " (cutoff:3.500A) Processing helix chain 'P' and resid 435 through 443 Processing helix chain 'Q' and resid 35 through 39 removed outlier: 3.796A pdb=" N GLY Q 38 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 58 removed outlier: 3.605A pdb=" N ALA Q 48 " --> pdb=" O ASN Q 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 88 removed outlier: 4.006A pdb=" N ALA Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 101 No H-bonds generated for 'chain 'Q' and resid 99 through 101' Processing helix chain 'Q' and resid 107 through 120 removed outlier: 3.756A pdb=" N ILE Q 120 " --> pdb=" O PHE Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 184 Processing helix chain 'Q' and resid 206 through 210 Processing helix chain 'Q' and resid 240 through 249 Processing helix chain 'Q' and resid 258 through 263 removed outlier: 4.026A pdb=" N GLN Q 262 " --> pdb=" O MET Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 271 through 278 Processing helix chain 'Q' and resid 278 through 290 removed outlier: 3.753A pdb=" N VAL Q 282 " --> pdb=" O GLU Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 303 through 307 Processing helix chain 'Q' and resid 308 through 319 Processing helix chain 'Q' and resid 351 through 356 Processing helix chain 'Q' and resid 367 through 382 Processing helix chain 'Q' and resid 387 through 401 removed outlier: 3.536A pdb=" N LYS Q 400 " --> pdb=" O GLU Q 396 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR Q 401 " --> pdb=" O ILE Q 397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 402 through 409 removed outlier: 3.512A pdb=" N LEU Q 409 " --> pdb=" O TYR Q 405 " (cutoff:3.500A) Processing helix chain 'Q' and resid 410 through 420 Processing helix chain 'Q' and resid 426 through 437 removed outlier: 3.603A pdb=" N VAL Q 430 " --> pdb=" O GLU Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 439 through 450 Processing helix chain 'R' and resid 49 through 66 Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 116 through 126 Processing helix chain 'R' and resid 175 through 186 Processing helix chain 'R' and resid 212 through 216 Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 254 through 259 removed outlier: 4.407A pdb=" N LEU R 258 " --> pdb=" O THR R 254 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA R 259 " --> pdb=" O GLN R 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 254 through 259' Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 274 through 287 Processing helix chain 'R' and resid 301 through 304 Processing helix chain 'R' and resid 305 through 316 removed outlier: 3.905A pdb=" N ARG R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 346 removed outlier: 3.533A pdb=" N ILE R 346 " --> pdb=" O PRO R 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 343 through 346' Processing helix chain 'R' and resid 347 through 352 Processing helix chain 'R' and resid 363 through 379 removed outlier: 3.797A pdb=" N LYS R 368 " --> pdb=" O GLU R 364 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU R 378 " --> pdb=" O ARG R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 395 Processing helix chain 'R' and resid 398 through 416 removed outlier: 3.677A pdb=" N ALA R 402 " --> pdb=" O SER R 398 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR R 407 " --> pdb=" O ILE R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 422 through 433 Processing helix chain 'R' and resid 435 through 443 Processing helix chain 'S' and resid 55 through 61 removed outlier: 3.624A pdb=" N LYS S 61 " --> pdb=" O GLU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 92 Processing helix chain 'S' and resid 97 through 101 Processing helix chain 'S' and resid 112 through 126 Processing helix chain 'S' and resid 137 through 146 Processing helix chain 'S' and resid 172 through 175 Processing helix chain 'S' and resid 181 through 197 Processing helix chain 'S' and resid 202 through 217 removed outlier: 3.511A pdb=" N GLU S 207 " --> pdb=" O THR S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 222 through 233 Processing helix chain 'S' and resid 252 through 257 Processing helix chain 'S' and resid 258 through 262 Processing helix chain 'S' and resid 273 through 285 Processing helix chain 'S' and resid 286 through 296 removed outlier: 4.400A pdb=" N LYS S 291 " --> pdb=" O VAL S 287 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 306 removed outlier: 4.044A pdb=" N TYR S 306 " --> pdb=" O THR S 303 " (cutoff:3.500A) Processing helix chain 'S' and resid 308 through 321 Processing helix chain 'S' and resid 334 through 336 No H-bonds generated for 'chain 'S' and resid 334 through 336' Processing helix chain 'S' and resid 337 through 349 Processing helix chain 'S' and resid 350 through 355 removed outlier: 4.040A pdb=" N GLN S 354 " --> pdb=" O THR S 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 359 through 366 Processing helix chain 'S' and resid 369 through 374 Processing helix chain 'T' and resid 95 through 109 Processing helix chain 'T' and resid 114 through 118 Processing helix chain 'T' and resid 129 through 143 Processing helix chain 'T' and resid 154 through 163 Processing helix chain 'T' and resid 189 through 192 Processing helix chain 'T' and resid 198 through 214 Processing helix chain 'T' and resid 219 through 221 No H-bonds generated for 'chain 'T' and resid 219 through 221' Processing helix chain 'T' and resid 247 through 267 Processing helix chain 'T' and resid 275 through 280 Processing helix chain 'T' and resid 299 through 304 removed outlier: 3.676A pdb=" N ILE T 304 " --> pdb=" O GLU T 300 " (cutoff:3.500A) Processing helix chain 'T' and resid 305 through 309 Processing helix chain 'T' and resid 310 through 314 removed outlier: 3.736A pdb=" N ASN T 313 " --> pdb=" O ASP T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 324 through 335 Processing helix chain 'T' and resid 340 through 347 Processing helix chain 'T' and resid 353 through 357 Processing helix chain 'T' and resid 359 through 372 Processing helix chain 'T' and resid 385 through 391 Processing helix chain 'T' and resid 391 through 402 Processing helix chain 'T' and resid 404 through 409 Processing helix chain 'T' and resid 413 through 420 Processing helix chain 'T' and resid 422 through 428 removed outlier: 4.269A pdb=" N ARG T 426 " --> pdb=" O GLN T 422 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 61 Processing helix chain 'U' and resid 81 through 90 removed outlier: 3.607A pdb=" N ILE U 85 " --> pdb=" O ASP U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 91 through 93 No H-bonds generated for 'chain 'U' and resid 91 through 93' Processing helix chain 'U' and resid 111 through 128 Processing helix chain 'U' and resid 136 through 143 removed outlier: 3.543A pdb=" N LEU U 140 " --> pdb=" O ILE U 136 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 175 Processing helix chain 'U' and resid 183 through 197 removed outlier: 3.678A pdb=" N ASP U 187 " --> pdb=" O ARG U 183 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 213 removed outlier: 5.683A pdb=" N ILE U 208 " --> pdb=" O ALA U 204 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL U 209 " --> pdb=" O GLU U 205 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS U 213 " --> pdb=" O VAL U 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 224 through 232 Processing helix chain 'U' and resid 258 through 262 removed outlier: 3.803A pdb=" N LEU U 261 " --> pdb=" O PRO U 258 " (cutoff:3.500A) Processing helix chain 'U' and resid 263 through 267 Processing helix chain 'U' and resid 273 through 285 Processing helix chain 'U' and resid 286 through 296 removed outlier: 3.991A pdb=" N LYS U 291 " --> pdb=" O VAL U 287 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP U 292 " --> pdb=" O ASP U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 306 removed outlier: 3.653A pdb=" N TYR U 306 " --> pdb=" O THR U 303 " (cutoff:3.500A) Processing helix chain 'U' and resid 308 through 321 Processing helix chain 'U' and resid 334 through 336 No H-bonds generated for 'chain 'U' and resid 334 through 336' Processing helix chain 'U' and resid 337 through 348 Processing helix chain 'U' and resid 349 through 356 removed outlier: 4.128A pdb=" N GLN U 353 " --> pdb=" O SER U 350 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN U 354 " --> pdb=" O THR U 351 " (cutoff:3.500A) Processing helix chain 'U' and resid 358 through 366 removed outlier: 4.092A pdb=" N GLU U 364 " --> pdb=" O GLN U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 367 through 369 No H-bonds generated for 'chain 'U' and resid 367 through 369' Processing helix chain 'V' and resid 54 through 63 Processing helix chain 'V' and resid 124 through 129 removed outlier: 3.875A pdb=" N ARG V 128 " --> pdb=" O PRO V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 139 through 146 Processing helix chain 'V' and resid 153 through 167 removed outlier: 3.756A pdb=" N HIS V 159 " --> pdb=" O ALA V 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 170 through 178 removed outlier: 3.947A pdb=" N ASP V 176 " --> pdb=" O VAL V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 187 through 204 removed outlier: 3.954A pdb=" N LEU V 191 " --> pdb=" O SER V 187 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA V 203 " --> pdb=" O CYS V 199 " (cutoff:3.500A) Processing helix chain 'V' and resid 220 through 235 removed outlier: 3.516A pdb=" N ARG V 225 " --> pdb=" O GLY V 221 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU V 230 " --> pdb=" O ARG V 226 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU V 233 " --> pdb=" O GLN V 229 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN V 235 " --> pdb=" O GLU V 231 " (cutoff:3.500A) Processing helix chain 'V' and resid 237 through 258 removed outlier: 4.523A pdb=" N VAL V 241 " --> pdb=" O THR V 237 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 61 Processing helix chain 'W' and resid 123 through 129 Processing helix chain 'W' and resid 148 through 157 Processing helix chain 'W' and resid 171 through 204 removed outlier: 3.780A pdb=" N LYS W 182 " --> pdb=" O LYS W 178 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA W 185 " --> pdb=" O GLU W 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 7.258A pdb=" N ARG A 43 " --> pdb=" O ILE B 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.712A pdb=" N ILE A 79 " --> pdb=" O GLY B 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.155A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'E' and resid 42 through 43 removed outlier: 6.891A pdb=" N ARG E 42 " --> pdb=" O ILE F 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.704A pdb=" N THR E 101 " --> pdb=" O TYR H 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.922A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'I' and resid 639 through 641 removed outlier: 6.432A pdb=" N ARG I 741 " --> pdb=" O ARG I 769 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU I 771 " --> pdb=" O ARG I 741 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU I 743 " --> pdb=" O LEU I 771 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU I 773 " --> pdb=" O LEU I 743 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU I 745 " --> pdb=" O LEU I 773 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE I 672 " --> pdb=" O THR I 723 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU I 696 " --> pdb=" O ILE I 722 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 857 through 859 removed outlier: 3.651A pdb=" N ILE I 857 " --> pdb=" O ARG I2165 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE I2167 " --> pdb=" O ILE I 857 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR I2164 " --> pdb=" O ASP I2131 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL I2133 " --> pdb=" O TYR I2164 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU I2166 " --> pdb=" O VAL I2133 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE I2135 " --> pdb=" O LEU I2166 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N SER I2168 " --> pdb=" O PHE I2135 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ARG I2061 " --> pdb=" O THR I2132 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL I2134 " --> pdb=" O ARG I2061 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU I2063 " --> pdb=" O VAL I2134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 916 through 917 removed outlier: 5.615A pdb=" N PHE I 916 " --> pdb=" O GLU I1984 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 212 through 214 removed outlier: 6.535A pdb=" N THR P 162 " --> pdb=" O VAL P 143 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE P 145 " --> pdb=" O LYS P 160 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS P 160 " --> pdb=" O ILE P 145 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE P 147 " --> pdb=" O VAL P 158 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL P 158 " --> pdb=" O ILE P 147 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY P 159 " --> pdb=" O LEU P 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 169 through 174 current: chain 'P' and resid 202 through 208 removed outlier: 8.146A pdb=" N VAL P 225 " --> pdb=" O LEU P 205 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG P 207 " --> pdb=" O VAL P 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 301 through 302 Processing sheet with id=AB6, first strand: chain 'K' and resid 13 through 16 Processing sheet with id=AB7, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AB8, first strand: chain 'K' and resid 121 through 122 Processing sheet with id=AB9, first strand: chain 'K' and resid 171 through 172 removed outlier: 8.134A pdb=" N VAL K 318 " --> pdb=" O CYS K 144 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE K 146 " --> pdb=" O VAL K 318 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR K 320 " --> pdb=" O ILE K 146 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL K 148 " --> pdb=" O THR K 320 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 236 through 237 Processing sheet with id=AC2, first strand: chain 'L' and resid 126 through 127 removed outlier: 3.645A pdb=" N TYR L 135 " --> pdb=" O TYR L 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AC4, first strand: chain 'M' and resid 93 through 97 Processing sheet with id=AC5, first strand: chain 'M' and resid 237 through 239 removed outlier: 3.624A pdb=" N VAL M 295 " --> pdb=" O GLY M 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 129 through 140 removed outlier: 5.855A pdb=" N VAL M 135 " --> pdb=" O LYS M 162 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS M 162 " --> pdb=" O VAL M 135 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU M 137 " --> pdb=" O GLY M 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 166 through 172 current: chain 'M' and resid 201 through 205 Processing sheet with id=AC7, first strand: chain 'M' and resid 336 through 337 Processing sheet with id=AC8, first strand: chain 'N' and resid 42 through 43 Processing sheet with id=AC9, first strand: chain 'N' and resid 100 through 104 Processing sheet with id=AD1, first strand: chain 'N' and resid 127 through 148 removed outlier: 6.609A pdb=" N THR N 162 " --> pdb=" O VAL N 143 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE N 145 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS N 160 " --> pdb=" O ILE N 145 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE N 147 " --> pdb=" O VAL N 158 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL N 158 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY N 159 " --> pdb=" O LEU N 174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 332 through 334 Processing sheet with id=AD3, first strand: chain 'O' and resid 35 through 36 Processing sheet with id=AD4, first strand: chain 'O' and resid 93 through 97 removed outlier: 6.372A pdb=" N VAL O 66 " --> pdb=" O PHE O 329 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER O 331 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU O 68 " --> pdb=" O SER O 331 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA O 65 " --> pdb=" O MET O 359 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE O 361 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU O 67 " --> pdb=" O ILE O 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 120 through 142 removed outlier: 6.489A pdb=" N GLY O 160 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU O 138 " --> pdb=" O ILE O 158 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE O 158 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N HIS O 156 " --> pdb=" O PRO O 140 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU O 142 " --> pdb=" O ILE O 154 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE O 154 " --> pdb=" O GLU O 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 167 through 172 current: chain 'O' and resid 200 through 206 removed outlier: 4.689A pdb=" N VAL O 221 " --> pdb=" O GLN O 203 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG O 205 " --> pdb=" O VAL O 221 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 335 through 337 removed outlier: 3.737A pdb=" N CYS O 336 " --> pdb=" O SER O 346 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 100 through 104 removed outlier: 6.184A pdb=" N LEU P 296 " --> pdb=" O ILE P 325 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA P 327 " --> pdb=" O LEU P 296 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE P 298 " --> pdb=" O ALA P 327 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL P 73 " --> pdb=" O MET P 326 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N THR P 328 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE P 75 " --> pdb=" O THR P 328 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ALA P 72 " --> pdb=" O LEU P 355 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL P 357 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU P 74 " --> pdb=" O VAL P 357 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR P 359 " --> pdb=" O LEU P 74 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA P 76 " --> pdb=" O THR P 359 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 128 through 133 Processing sheet with id=AD9, first strand: chain 'P' and resid 333 through 334 Processing sheet with id=AE1, first strand: chain 'Q' and resid 93 through 97 removed outlier: 3.532A pdb=" N ASP Q 302 " --> pdb=" O MET Q 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 229 through 239 removed outlier: 3.801A pdb=" N LYS Q 232 " --> pdb=" O LYS Q 128 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS Q 128 " --> pdb=" O LYS Q 232 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 167 through 172 removed outlier: 6.356A pdb=" N ILE Q 154 " --> pdb=" O GLU Q 142 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU Q 142 " --> pdb=" O ILE Q 154 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS Q 156 " --> pdb=" O PRO Q 140 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE Q 158 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU Q 138 " --> pdb=" O ILE Q 158 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY Q 160 " --> pdb=" O THR Q 136 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY Q 133 " --> pdb=" O ILE Q 191 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE Q 191 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY Q 204 " --> pdb=" O VAL Q 190 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR Q 192 " --> pdb=" O ARG Q 202 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG Q 202 " --> pdb=" O TYR Q 192 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 335 through 337 Processing sheet with id=AE5, first strand: chain 'R' and resid 100 through 104 Processing sheet with id=AE6, first strand: chain 'R' and resid 127 through 147 removed outlier: 6.598A pdb=" N THR R 162 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE R 145 " --> pdb=" O LYS R 160 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS R 160 " --> pdb=" O ILE R 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 333 through 334 Processing sheet with id=AE8, first strand: chain 'R' and resid 381 through 382 removed outlier: 7.111A pdb=" N GLU R 381 " --> pdb=" O VAL R 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'S' and resid 29 through 32 removed outlier: 4.350A pdb=" N ASN S 12 " --> pdb=" O THR S 106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 53 through 54 Processing sheet with id=AF2, first strand: chain 'S' and resid 71 through 72 Processing sheet with id=AF3, first strand: chain 'S' and resid 149 through 155 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 169 through 170 current: chain 'S' and resid 329 through 330 Processing sheet with id=AF4, first strand: chain 'S' and resid 238 through 241 Processing sheet with id=AF5, first strand: chain 'T' and resid 35 through 38 removed outlier: 5.007A pdb=" N ILE T 18 " --> pdb=" O SER T 123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 88 through 89 Processing sheet with id=AF7, first strand: chain 'T' and resid 167 through 172 Processing sheet with id=AF8, first strand: chain 'T' and resid 223 through 226 removed outlier: 6.671A pdb=" N LYS T 238 " --> pdb=" O ALA T 224 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 285 through 288 Processing sheet with id=AG1, first strand: chain 'U' and resid 20 through 21 removed outlier: 4.389A pdb=" N GLY U 20 " --> pdb=" O VAL U 9 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL U 9 " --> pdb=" O GLY U 20 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU U 8 " --> pdb=" O LEU U 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'U' and resid 53 through 54 Processing sheet with id=AG3, first strand: chain 'U' and resid 149 through 150 Processing sheet with id=AG4, first strand: chain 'U' and resid 160 through 161 Processing sheet with id=AG5, first strand: chain 'V' and resid 96 through 101 Processing sheet with id=AG6, first strand: chain 'W' and resid 86 through 92 Processing sheet with id=AG7, first strand: chain 'W' and resid 78 through 81 removed outlier: 3.572A pdb=" N LYS W 65 " --> pdb=" O PHE W 103 " (cutoff:3.500A) 2353 hydrogen bonds defined for protein. 6651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 280 hydrogen bonds 560 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 217 stacking parallelities Total time for adding SS restraints: 25.27 Time building geometry restraints manager: 13.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9548 1.33 - 1.45: 15111 1.45 - 1.57: 31399 1.57 - 1.69: 574 1.69 - 1.81: 418 Bond restraints: 57050 Sorted by residual: bond pdb=" C4 ATP U 401 " pdb=" C5 ATP U 401 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.93e+01 bond pdb=" C4 ATP T 501 " pdb=" C5 ATP T 501 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.27e+01 bond pdb=" C5 ATP U 401 " pdb=" C6 ATP U 401 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.81e+01 bond pdb=" C4 ATP T 501 " pdb=" N9 ATP T 501 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" C5 ATP T 501 " pdb=" N7 ATP T 501 " ideal model delta sigma weight residual 1.387 1.335 0.052 1.00e-02 1.00e+04 2.65e+01 ... (remaining 57045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.21: 78149 5.21 - 10.42: 82 10.42 - 15.63: 7 15.63 - 20.84: 1 20.84 - 26.05: 4 Bond angle restraints: 78243 Sorted by residual: angle pdb=" PB ATP U 401 " pdb=" O3B ATP U 401 " pdb=" PG ATP U 401 " ideal model delta sigma weight residual 139.87 113.82 26.05 1.00e+00 1.00e+00 6.79e+02 angle pdb=" PA ATP U 401 " pdb=" O3A ATP U 401 " pdb=" PB ATP U 401 " ideal model delta sigma weight residual 136.83 113.16 23.67 1.00e+00 1.00e+00 5.60e+02 angle pdb=" PB ATP T 501 " pdb=" O3B ATP T 501 " pdb=" PG ATP T 501 " ideal model delta sigma weight residual 139.87 116.37 23.50 1.00e+00 1.00e+00 5.52e+02 angle pdb=" PA ATP T 501 " pdb=" O3A ATP T 501 " pdb=" PB ATP T 501 " ideal model delta sigma weight residual 136.83 114.34 22.49 1.00e+00 1.00e+00 5.06e+02 angle pdb=" CA PRO J 283 " pdb=" N PRO J 283 " pdb=" CD PRO J 283 " ideal model delta sigma weight residual 112.00 99.68 12.32 1.40e+00 5.10e-01 7.75e+01 ... (remaining 78238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 32288 34.65 - 69.31: 1785 69.31 - 103.96: 55 103.96 - 138.62: 6 138.62 - 173.27: 1 Dihedral angle restraints: 34135 sinusoidal: 15960 harmonic: 18175 Sorted by residual: dihedral pdb=" CA THR W 170 " pdb=" C THR W 170 " pdb=" N GLU W 171 " pdb=" CA GLU W 171 " ideal model delta harmonic sigma weight residual -180.00 -62.91 -117.09 0 5.00e+00 4.00e-02 5.48e+02 dihedral pdb=" CA CYS U 257 " pdb=" C CYS U 257 " pdb=" N PRO U 258 " pdb=" CA PRO U 258 " ideal model delta harmonic sigma weight residual 180.00 130.78 49.22 0 5.00e+00 4.00e-02 9.69e+01 dihedral pdb=" CD ARG I 163 " pdb=" NE ARG I 163 " pdb=" CZ ARG I 163 " pdb=" NH1 ARG I 163 " ideal model delta sinusoidal sigma weight residual 0.00 89.01 -89.01 1 1.00e+01 1.00e-02 9.43e+01 ... (remaining 34132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 8813 0.321 - 0.642: 13 0.642 - 0.962: 0 0.962 - 1.283: 0 1.283 - 1.604: 1 Chirality restraints: 8827 Sorted by residual: chirality pdb=" CB ILE M 234 " pdb=" CA ILE M 234 " pdb=" CG1 ILE M 234 " pdb=" CG2 ILE M 234 " both_signs ideal model delta sigma weight residual False 2.64 1.04 1.60 2.00e-01 2.50e+01 6.43e+01 chirality pdb=" P DT Y -4 " pdb=" OP1 DT Y -4 " pdb=" OP2 DT Y -4 " pdb=" O5' DT Y -4 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.94e+00 chirality pdb=" P DA X 4 " pdb=" OP1 DA X 4 " pdb=" OP2 DA X 4 " pdb=" O5' DA X 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 8824 not shown) Planarity restraints: 9069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 163 " -1.101 9.50e-02 1.11e+02 4.93e-01 1.47e+02 pdb=" NE ARG I 163 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG I 163 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG I 163 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG I 163 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 260 " -1.074 9.50e-02 1.11e+02 4.81e-01 1.40e+02 pdb=" NE ARG J 260 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG J 260 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 260 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 260 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 167 " 0.941 9.50e-02 1.11e+02 4.22e-01 1.08e+02 pdb=" NE ARG I 167 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG I 167 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG I 167 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG I 167 " 0.023 2.00e-02 2.50e+03 ... (remaining 9066 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.91: 26 1.91 - 2.66: 1276 2.66 - 3.41: 78908 3.41 - 4.15: 137810 4.15 - 4.90: 242609 Nonbonded interactions: 460629 Sorted by model distance: nonbonded pdb=" NH2 ARG A 43 " pdb=" O3' DC Y -35 " model vdw 1.169 3.120 nonbonded pdb=" O THR M 74 " pdb=" O3B ADP M 501 " model vdw 1.294 3.040 nonbonded pdb=" NH1 ARG B 28 " pdb=" OP1 DA Y -22 " model vdw 1.311 3.120 nonbonded pdb=" CG ARG I 736 " pdb=" OP1 DG Y-130 " model vdw 1.314 3.440 nonbonded pdb=" CZ ARG A 43 " pdb=" O3' DC Y -35 " model vdw 1.372 3.270 ... (remaining 460624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 119) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 28 through 121) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 41 through 134) selection = (chain 'G' and resid 41 through 134) } ncs_group { reference = (chain 'D' and resid 23 through 102) selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 15 through 451 or resid 501)) selection = (chain 'O' and (resid 15 through 141 or resid 153 through 209 or resid 220 throu \ gh 451 or resid 501)) selection = (chain 'Q' and (resid 15 through 141 or resid 153 through 209 or resid 220 throu \ gh 451 or resid 501)) } ncs_group { reference = (chain 'N' and (resid 18 through 148 or resid 157 through 447 or resid 501)) selection = (chain 'P' and (resid 18 through 148 or resid 157 through 208 or resid 225 throu \ gh 447 or resid 501)) selection = (chain 'R' and (resid 18 through 208 or resid 225 through 447 or resid 501)) } ncs_group { reference = (chain 'S' and (resid 2 through 40 or resid 52 through 371)) selection = (chain 'U' and resid 2 through 371) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.630 Check model and map are aligned: 0.310 Set scattering table: 0.420 Process input model: 109.380 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4351 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 : 0.004 0.149 57050 Z= 0.233 Angle : 0.685 26.050 78243 Z= 0.439 Chirality : 0.047 1.604 8827 Planarity : 0.011 0.493 9069 Dihedral : 17.101 173.273 22401 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.58 % Favored : 95.21 % Rotamer: Outliers : 4.96 % Allowed : 5.79 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.10), residues: 6201 helix: -0.57 (0.09), residues: 2880 sheet: -1.86 (0.17), residues: 761 loop : -2.16 (0.11), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 667 HIS 0.008 0.001 HIS M 316 PHE 0.016 0.001 PHE W 68 TYR 0.017 0.001 TYR V 246 ARG 0.006 0.000 ARG K 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1065 time to evaluate : 4.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 37 LYS cc_start: 0.3824 (ptpt) cc_final: 0.3469 (mmtp) REVERT: F 30 ARG cc_start: -0.0803 (OUTLIER) cc_final: -0.1715 (mtp-110) REVERT: I 95 GLU cc_start: -0.0982 (OUTLIER) cc_final: -0.1625 (tt0) REVERT: I 99 GLN cc_start: -0.2431 (OUTLIER) cc_final: -0.2711 (mt0) REVERT: I 136 HIS cc_start: 0.0276 (OUTLIER) cc_final: -0.0417 (t-170) REVERT: I 789 MET cc_start: 0.2012 (ttp) cc_final: 0.1040 (ppp) REVERT: I 2060 HIS cc_start: 0.5510 (m-70) cc_final: 0.5182 (m170) REVERT: I 2185 MET cc_start: 0.4439 (mmm) cc_final: 0.4196 (tpp) REVERT: I 2189 MET cc_start: 0.3765 (mmm) cc_final: 0.3027 (ttm) REVERT: J 182 LEU cc_start: 0.4794 (mt) cc_final: 0.4376 (tt) REVERT: J 190 TYR cc_start: 0.3363 (t80) cc_final: 0.3116 (t80) REVERT: K 22 VAL cc_start: 0.6758 (t) cc_final: 0.6363 (m) REVERT: K 269 ARG cc_start: 0.4362 (OUTLIER) cc_final: 0.3060 (mmm-85) REVERT: K 309 MET cc_start: 0.7431 (mpt) cc_final: 0.7129 (mmt) REVERT: K 319 LEU cc_start: 0.7531 (mt) cc_final: 0.7163 (mt) REVERT: K 336 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: L 1 MET cc_start: 0.1117 (mtt) cc_final: 0.0417 (tpt) REVERT: L 37 ASN cc_start: 0.6038 (t0) cc_final: 0.5518 (p0) REVERT: L 153 THR cc_start: 0.1966 (p) cc_final: 0.1747 (p) REVERT: M 236 GLN cc_start: 0.6500 (tt0) cc_final: 0.6145 (mt0) REVERT: M 323 ILE cc_start: 0.8669 (pp) cc_final: 0.8392 (mp) REVERT: M 363 THR cc_start: 0.8321 (m) cc_final: 0.7801 (p) REVERT: M 414 ASN cc_start: 0.6762 (t0) cc_final: 0.6550 (t0) REVERT: N 120 THR cc_start: 0.7281 (OUTLIER) cc_final: 0.6846 (t) REVERT: N 133 GLU cc_start: 0.6719 (tp30) cc_final: 0.6110 (tp30) REVERT: N 372 ARG cc_start: 0.7159 (mtt180) cc_final: 0.6945 (mtt90) REVERT: N 389 VAL cc_start: 0.7275 (t) cc_final: 0.6943 (p) REVERT: O 64 ARG cc_start: 0.7014 (mmt-90) cc_final: 0.6417 (mmm-85) REVERT: O 285 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.6062 (mttp) REVERT: P 265 THR cc_start: 0.4218 (OUTLIER) cc_final: 0.3941 (m) REVERT: P 269 LYS cc_start: 0.7947 (ttpp) cc_final: 0.7461 (pttp) REVERT: P 380 VAL cc_start: 0.8279 (t) cc_final: 0.8005 (p) REVERT: P 404 GLN cc_start: 0.7570 (mt0) cc_final: 0.7360 (mt0) REVERT: Q 110 GLU cc_start: 0.6313 (tp30) cc_final: 0.6020 (tp30) REVERT: Q 181 GLN cc_start: 0.6225 (OUTLIER) cc_final: 0.5353 (mt0) REVERT: Q 201 LYS cc_start: 0.7692 (tptm) cc_final: 0.7352 (ttpt) REVERT: Q 220 TYR cc_start: 0.1160 (OUTLIER) cc_final: 0.0464 (t80) REVERT: Q 346 SER cc_start: 0.8989 (m) cc_final: 0.8396 (t) REVERT: R 62 MET cc_start: 0.8095 (ttp) cc_final: 0.7866 (ttp) REVERT: R 88 MET cc_start: 0.7748 (mmm) cc_final: 0.7390 (mmm) REVERT: R 193 ILE cc_start: 0.7278 (tp) cc_final: 0.6064 (tp) REVERT: R 232 LEU cc_start: 0.6070 (tp) cc_final: 0.5719 (tt) REVERT: R 253 ARG cc_start: 0.6733 (tpp80) cc_final: 0.6449 (ttp-110) REVERT: R 446 TYR cc_start: 0.6076 (m-80) cc_final: 0.5574 (m-10) REVERT: S 121 GLN cc_start: 0.3026 (tt0) cc_final: 0.2734 (mt0) REVERT: S 123 MET cc_start: 0.2469 (mmt) cc_final: 0.2099 (ttt) REVERT: S 132 MET cc_start: 0.0824 (ptm) cc_final: 0.0378 (ptm) REVERT: S 153 MET cc_start: 0.0617 (tmm) cc_final: -0.0229 (mpp) REVERT: S 271 SER cc_start: 0.3336 (m) cc_final: 0.2999 (p) REVERT: T 82 MET cc_start: 0.0478 (mmt) cc_final: 0.0076 (mmm) REVERT: T 410 TRP cc_start: 0.0207 (m100) cc_final: -0.0212 (m100) REVERT: U 318 THR cc_start: 0.5930 (OUTLIER) cc_final: 0.5569 (m) REVERT: V 229 GLN cc_start: 0.2991 (OUTLIER) cc_final: 0.2597 (tm-30) REVERT: V 253 LYS cc_start: 0.3563 (OUTLIER) cc_final: 0.1706 (tptt) outliers start: 267 outliers final: 36 residues processed: 1263 average time/residue: 0.5783 time to fit residues: 1174.9176 Evaluate side-chains 550 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 500 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1885 TYR Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 268 PHE Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 370 ASP Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 393 HIS Chi-restraints excluded: chain N residue 120 THR Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 291 ILE Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 404 ARG Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 318 THR Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 229 GLN Chi-restraints excluded: chain V residue 253 LYS Chi-restraints excluded: chain W residue 170 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 542 optimal weight: 20.0000 chunk 487 optimal weight: 0.9980 chunk 270 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 260 optimal weight: 0.6980 chunk 503 optimal weight: 30.0000 chunk 195 optimal weight: 0.9990 chunk 306 optimal weight: 0.9990 chunk 375 optimal weight: 1.9990 chunk 583 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN B 44 GLN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS F 44 GLN F 46 HIS F 81 ASN F 92 GLN I 99 GLN I 172 HIS I 178 GLN I 204 GLN I 903 HIS I 936 HIS I 967 HIS I1896 GLN I1968 GLN I2060 HIS I2099 GLN J 202 HIS J 330 HIS K 8 ASN K 194 HIS K 204 GLN ** K 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN M 332 ASN M 414 ASN N 240 HIS N 275 GLN N 302 HIS N 447 GLN O 156 HIS ** O 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 373 GLN O 393 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 44 GLN Q 18 HIS Q 42 GLN Q 115 ASN Q 229 HIS R 25 HIS R 255 GLN R 302 HIS ** R 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 252 ASN T 277 GLN T 354 ASN ** T 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 GLN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 353 GLN V 249 GLN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4587 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 57050 Z= 0.241 Angle : 0.675 12.944 78243 Z= 0.348 Chirality : 0.044 0.267 8827 Planarity : 0.006 0.140 9069 Dihedral : 20.274 170.078 10095 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 2.71 % Allowed : 11.76 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.10), residues: 6201 helix: 0.39 (0.10), residues: 2879 sheet: -1.15 (0.17), residues: 742 loop : -1.44 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 250 HIS 0.012 0.001 HIS K 156 PHE 0.025 0.002 PHE V 129 TYR 0.021 0.002 TYR R 387 ARG 0.010 0.001 ARG I 866 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 551 time to evaluate : 4.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.4188 (ptpt) cc_final: 0.3678 (mmtp) REVERT: I 136 HIS cc_start: 0.1088 (OUTLIER) cc_final: 0.0396 (t-170) REVERT: I 789 MET cc_start: 0.2387 (ttp) cc_final: 0.1289 (ppp) REVERT: I 1972 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8418 (pt) REVERT: I 2068 MET cc_start: 0.5842 (mtm) cc_final: 0.5542 (mtm) REVERT: I 2072 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6571 (mp) REVERT: I 2185 MET cc_start: 0.4511 (mmm) cc_final: 0.4226 (tpp) REVERT: I 2189 MET cc_start: 0.3787 (mmm) cc_final: 0.3119 (ptm) REVERT: J 190 TYR cc_start: 0.3322 (t80) cc_final: 0.3114 (t80) REVERT: K 7 ASP cc_start: 0.6331 (OUTLIER) cc_final: 0.5963 (p0) REVERT: K 8 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.6994 (t0) REVERT: K 64 TYR cc_start: 0.3799 (m-80) cc_final: 0.3589 (m-10) REVERT: K 78 LEU cc_start: 0.8458 (mt) cc_final: 0.8250 (mt) REVERT: K 309 MET cc_start: 0.7287 (mpt) cc_final: 0.7078 (mmt) REVERT: L 1 MET cc_start: 0.0942 (mtt) cc_final: 0.0296 (tpt) REVERT: M 293 GLU cc_start: 0.7329 (tp30) cc_final: 0.7052 (tt0) REVERT: M 392 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7987 (m-40) REVERT: N 171 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8259 (tt) REVERT: N 254 THR cc_start: 0.8624 (m) cc_final: 0.8419 (t) REVERT: N 276 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7318 (mp) REVERT: N 387 TYR cc_start: 0.7910 (m-80) cc_final: 0.7587 (m-80) REVERT: O 18 HIS cc_start: 0.7096 (m-70) cc_final: 0.6822 (m-70) REVERT: O 61 MET cc_start: 0.8639 (tpp) cc_final: 0.8422 (tpp) REVERT: O 285 LYS cc_start: 0.6656 (OUTLIER) cc_final: 0.6394 (mttp) REVERT: O 356 ASP cc_start: 0.7283 (t70) cc_final: 0.6958 (t0) REVERT: O 392 ASN cc_start: 0.7823 (t0) cc_final: 0.7562 (p0) REVERT: P 178 MET cc_start: 0.8704 (tpp) cc_final: 0.7780 (tpp) REVERT: P 380 VAL cc_start: 0.8255 (t) cc_final: 0.7917 (p) REVERT: P 404 GLN cc_start: 0.7942 (mt0) cc_final: 0.7723 (mt0) REVERT: Q 186 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7480 (pm20) REVERT: Q 201 LYS cc_start: 0.7764 (tptm) cc_final: 0.7390 (ttpt) REVERT: Q 220 TYR cc_start: 0.1014 (OUTLIER) cc_final: 0.0462 (t80) REVERT: Q 346 SER cc_start: 0.8915 (m) cc_final: 0.8523 (t) REVERT: Q 408 GLN cc_start: 0.8016 (mt0) cc_final: 0.7726 (mt0) REVERT: R 88 MET cc_start: 0.7781 (mmm) cc_final: 0.7452 (mmm) REVERT: R 382 MET cc_start: 0.8119 (ttm) cc_final: 0.7854 (ttt) REVERT: S 16 MET cc_start: 0.3956 (mpp) cc_final: 0.3638 (mpp) REVERT: S 121 GLN cc_start: 0.3164 (tt0) cc_final: 0.2776 (mt0) REVERT: S 123 MET cc_start: 0.3175 (mmt) cc_final: 0.2583 (ttt) REVERT: S 132 MET cc_start: 0.1575 (ptm) cc_final: 0.0818 (ptm) REVERT: S 153 MET cc_start: 0.0323 (tmm) cc_final: -0.0320 (mpp) REVERT: T 109 MET cc_start: 0.3378 (ttm) cc_final: 0.2830 (ttm) REVERT: T 222 MET cc_start: 0.1576 (tmm) cc_final: 0.0118 (ppp) REVERT: T 322 MET cc_start: 0.0132 (mpp) cc_final: -0.1676 (ttm) REVERT: T 410 TRP cc_start: 0.0591 (m100) cc_final: 0.0202 (m100) REVERT: V 137 VAL cc_start: 0.2689 (OUTLIER) cc_final: 0.2386 (m) REVERT: V 253 LYS cc_start: 0.3222 (OUTLIER) cc_final: 0.1854 (mmmt) outliers start: 146 outliers final: 64 residues processed: 669 average time/residue: 0.5247 time to fit residues: 596.7822 Evaluate side-chains 493 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 417 time to evaluate : 4.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 858 ARG Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1914 LEU Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2072 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 268 PHE Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 190 TYR Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 392 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 44 ASN Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 375 CYS Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 191 ILE Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 253 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 324 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 485 optimal weight: 0.9980 chunk 397 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 584 optimal weight: 0.6980 chunk 631 optimal weight: 20.0000 chunk 520 optimal weight: 30.0000 chunk 580 optimal weight: 0.0870 chunk 199 optimal weight: 0.6980 chunk 469 optimal weight: 20.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 232 HIS ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 HIS M 305 HIS O 169 GLN O 251 GLN ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 289 GLN Q 429 HIS R 447 GLN T 143 HIS T 277 GLN T 383 ASN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 296 ASN V 240 GLN ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4619 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 57050 Z= 0.187 Angle : 0.591 12.168 78243 Z= 0.306 Chirality : 0.041 0.418 8827 Planarity : 0.005 0.091 9069 Dihedral : 20.071 170.489 10040 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 2.51 % Allowed : 12.57 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.11), residues: 6201 helix: 0.79 (0.10), residues: 2907 sheet: -0.93 (0.17), residues: 756 loop : -1.17 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 250 HIS 0.009 0.001 HIS S 88 PHE 0.029 0.001 PHE P 257 TYR 0.028 0.001 TYR K 17 ARG 0.008 0.000 ARG I 866 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 430 time to evaluate : 4.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.4168 (ptpt) cc_final: 0.3671 (mmtp) REVERT: D 43 VAL cc_start: -0.0844 (t) cc_final: -0.1209 (t) REVERT: I 136 HIS cc_start: 0.0792 (OUTLIER) cc_final: 0.0112 (t-170) REVERT: I 789 MET cc_start: 0.2340 (ttp) cc_final: 0.1253 (ppp) REVERT: I 1914 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8037 (pp) REVERT: I 2068 MET cc_start: 0.6217 (mtm) cc_final: 0.5956 (mtm) REVERT: I 2072 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6812 (mp) REVERT: I 2185 MET cc_start: 0.4516 (mmm) cc_final: 0.4232 (tpp) REVERT: I 2189 MET cc_start: 0.4053 (mmm) cc_final: 0.3269 (ptm) REVERT: J 187 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4890 (mt) REVERT: J 190 TYR cc_start: 0.3329 (t80) cc_final: 0.3101 (t80) REVERT: K 233 MET cc_start: 0.7043 (tpt) cc_final: 0.6720 (tpt) REVERT: K 309 MET cc_start: 0.7501 (mpt) cc_final: 0.7146 (mmt) REVERT: L 1 MET cc_start: 0.0882 (mtt) cc_final: 0.0199 (tpt) REVERT: M 389 GLU cc_start: 0.7911 (tp30) cc_final: 0.7697 (tp30) REVERT: M 438 TYR cc_start: 0.7067 (m-80) cc_final: 0.6769 (m-80) REVERT: N 171 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8218 (tt) REVERT: N 261 PHE cc_start: 0.7758 (p90) cc_final: 0.7539 (p90) REVERT: N 276 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7251 (mp) REVERT: O 285 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6549 (mttp) REVERT: O 455 MET cc_start: 0.6747 (mmm) cc_final: 0.6483 (mmm) REVERT: P 168 MET cc_start: 0.8128 (ppp) cc_final: 0.7761 (ppp) REVERT: P 178 MET cc_start: 0.8736 (tpp) cc_final: 0.7527 (tpp) REVERT: P 404 GLN cc_start: 0.8005 (mt0) cc_final: 0.7768 (mt0) REVERT: Q 61 MET cc_start: 0.8392 (tpp) cc_final: 0.8061 (tpt) REVERT: Q 186 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7469 (pm20) REVERT: Q 220 TYR cc_start: 0.1109 (OUTLIER) cc_final: 0.0438 (t80) REVERT: Q 346 SER cc_start: 0.8977 (m) cc_final: 0.8493 (t) REVERT: Q 408 GLN cc_start: 0.8114 (mt0) cc_final: 0.7759 (mt0) REVERT: R 88 MET cc_start: 0.7781 (mmm) cc_final: 0.7447 (mmm) REVERT: R 90 MET cc_start: 0.8447 (mtp) cc_final: 0.7968 (mtp) REVERT: R 291 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8533 (mp) REVERT: S 121 GLN cc_start: 0.2936 (tt0) cc_final: 0.2673 (mt0) REVERT: S 123 MET cc_start: 0.3269 (mmt) cc_final: 0.2579 (ttt) REVERT: S 132 MET cc_start: 0.1593 (ptm) cc_final: 0.0805 (ptm) REVERT: T 109 MET cc_start: 0.3403 (ttm) cc_final: 0.2873 (ttm) REVERT: T 222 MET cc_start: 0.1512 (tmm) cc_final: 0.0078 (ppp) REVERT: T 282 MET cc_start: 0.0164 (ppp) cc_final: -0.2396 (mtt) REVERT: T 322 MET cc_start: -0.0066 (mpp) cc_final: -0.1693 (ttm) REVERT: T 410 TRP cc_start: 0.0311 (m100) cc_final: -0.0101 (m100) REVERT: U 185 LEU cc_start: -0.0719 (OUTLIER) cc_final: -0.1438 (mt) REVERT: V 253 LYS cc_start: 0.3215 (OUTLIER) cc_final: 0.1826 (mmmt) outliers start: 135 outliers final: 70 residues processed: 536 average time/residue: 0.5521 time to fit residues: 514.1705 Evaluate side-chains 462 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 381 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 990 VAL Chi-restraints excluded: chain I residue 1914 LEU Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2072 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 268 PHE Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 190 TYR Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 105 CYS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 44 ASN Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 206 CYS Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 145 ILE Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 191 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain T residue 285 VAL Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain T residue 362 ASP Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 296 ASN Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 253 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 577 optimal weight: 3.9990 chunk 439 optimal weight: 4.9990 chunk 303 optimal weight: 0.2980 chunk 64 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 392 optimal weight: 0.0020 chunk 587 optimal weight: 30.0000 chunk 621 optimal weight: 20.0000 chunk 306 optimal weight: 1.9990 chunk 556 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN I 145 GLN I1968 GLN K 8 ASN K 21 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 272 ASN K 283 ASN ** K 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN M 393 HIS O 241 HIS O 392 ASN ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 344 HIS ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 236 GLN Q 284 ASN ** S 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN T 407 GLN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 101 HIS ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4757 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 57050 Z= 0.260 Angle : 0.645 13.312 78243 Z= 0.331 Chirality : 0.043 0.277 8827 Planarity : 0.005 0.079 9069 Dihedral : 20.072 172.374 10036 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.82 % Favored : 95.16 % Rotamer: Outliers : 3.06 % Allowed : 13.08 % Favored : 83.86 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 6201 helix: 0.92 (0.10), residues: 2903 sheet: -0.70 (0.18), residues: 787 loop : -1.08 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP T 250 HIS 0.029 0.001 HIS I1991 PHE 0.029 0.002 PHE P 257 TYR 0.025 0.002 TYR C 99 ARG 0.028 0.001 ARG J 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 413 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 GLU cc_start: 0.3463 (mp0) cc_final: 0.3003 (mm-30) REVERT: I 136 HIS cc_start: 0.1070 (OUTLIER) cc_final: 0.0315 (t-170) REVERT: I 645 MET cc_start: 0.3761 (pmm) cc_final: 0.3337 (mmp) REVERT: I 789 MET cc_start: 0.2880 (ttp) cc_final: 0.1644 (ppp) REVERT: I 886 HIS cc_start: 0.4295 (m90) cc_final: 0.4054 (m170) REVERT: I 1972 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8565 (pp) REVERT: I 2063 LEU cc_start: 0.6989 (mp) cc_final: 0.6760 (mt) REVERT: I 2068 MET cc_start: 0.6465 (mtm) cc_final: 0.6169 (mtm) REVERT: I 2185 MET cc_start: 0.4575 (mmm) cc_final: 0.3992 (tpp) REVERT: I 2189 MET cc_start: 0.4273 (mmm) cc_final: 0.3403 (ptm) REVERT: J 187 LEU cc_start: 0.5256 (OUTLIER) cc_final: 0.4998 (mt) REVERT: J 190 TYR cc_start: 0.3727 (t80) cc_final: 0.3400 (t80) REVERT: K 1 MET cc_start: 0.6388 (tmm) cc_final: 0.5840 (tmm) REVERT: K 233 MET cc_start: 0.7914 (tpt) cc_final: 0.7695 (tpt) REVERT: K 269 ARG cc_start: 0.4481 (OUTLIER) cc_final: 0.3967 (mmm-85) REVERT: M 165 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7642 (mptt) REVERT: M 227 ASP cc_start: 0.7522 (t0) cc_final: 0.7177 (m-30) REVERT: M 389 GLU cc_start: 0.7954 (tp30) cc_final: 0.7651 (tp30) REVERT: M 408 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: N 113 MET cc_start: 0.8447 (ptp) cc_final: 0.7982 (ptp) REVERT: N 121 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6992 (mt0) REVERT: N 178 MET cc_start: 0.6832 (mmt) cc_final: 0.6525 (mmt) REVERT: N 276 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7204 (mp) REVERT: O 134 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6756 (tm-30) REVERT: O 135 VAL cc_start: 0.6008 (OUTLIER) cc_final: 0.5606 (m) REVERT: O 285 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6927 (mttp) REVERT: O 455 MET cc_start: 0.7702 (mmm) cc_final: 0.7320 (mmm) REVERT: P 167 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7834 (pp20) REVERT: Q 61 MET cc_start: 0.8235 (tpp) cc_final: 0.7852 (tpp) REVERT: Q 186 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7550 (pm20) REVERT: Q 220 TYR cc_start: 0.1151 (OUTLIER) cc_final: 0.0789 (t80) REVERT: Q 343 ASP cc_start: 0.8441 (t0) cc_final: 0.7914 (m-30) REVERT: Q 356 ASP cc_start: 0.8221 (t0) cc_final: 0.7915 (t0) REVERT: R 88 MET cc_start: 0.7797 (mmm) cc_final: 0.7413 (mmm) REVERT: R 193 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7637 (tp) REVERT: R 292 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8047 (pt) REVERT: R 326 MET cc_start: 0.8808 (mtm) cc_final: 0.8481 (mtm) REVERT: S 121 GLN cc_start: 0.3000 (tt0) cc_final: 0.2671 (mt0) REVERT: S 123 MET cc_start: 0.3947 (mmt) cc_final: 0.3032 (ttt) REVERT: S 132 MET cc_start: 0.1890 (ptm) cc_final: 0.0786 (ptm) REVERT: T 109 MET cc_start: 0.3351 (ttm) cc_final: 0.2804 (ttm) REVERT: T 282 MET cc_start: 0.0109 (ppp) cc_final: -0.2403 (mtt) REVERT: T 322 MET cc_start: 0.0269 (mpp) cc_final: -0.1443 (ttm) REVERT: T 410 TRP cc_start: 0.0437 (m100) cc_final: 0.0028 (m100) REVERT: U 82 MET cc_start: 0.1815 (mmm) cc_final: 0.1587 (tmm) REVERT: U 185 LEU cc_start: -0.0550 (OUTLIER) cc_final: -0.1451 (mt) REVERT: V 253 LYS cc_start: 0.2880 (mttt) cc_final: 0.1848 (mmmt) outliers start: 165 outliers final: 89 residues processed: 552 average time/residue: 0.4970 time to fit residues: 474.6651 Evaluate side-chains 457 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 353 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1914 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2050 VAL Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2139 ASP Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 268 PHE Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 190 TYR Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 385 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 206 CYS Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 191 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain T residue 376 MET Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain W residue 29 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 517 optimal weight: 9.9990 chunk 352 optimal weight: 1.9990 chunk 9 optimal weight: 0.0670 chunk 462 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 530 optimal weight: 5.9990 chunk 429 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 317 optimal weight: 7.9990 chunk 557 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN I 902 ASN J 183 ASN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN K 303 GLN M 420 ASN O 348 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 348 HIS R 302 HIS S 173 HIS T 251 HIS T 277 GLN ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4879 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 57050 Z= 0.439 Angle : 0.743 15.438 78243 Z= 0.381 Chirality : 0.047 0.289 8827 Planarity : 0.006 0.093 9069 Dihedral : 20.229 173.256 10027 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 3.71 % Allowed : 13.73 % Favored : 82.56 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 6201 helix: 0.77 (0.10), residues: 2920 sheet: -0.56 (0.18), residues: 772 loop : -1.24 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 250 HIS 0.010 0.002 HIS S 88 PHE 0.029 0.002 PHE L 116 TYR 0.022 0.002 TYR J 323 ARG 0.010 0.001 ARG R 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 368 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 136 HIS cc_start: 0.1076 (OUTLIER) cc_final: 0.0366 (t-170) REVERT: I 789 MET cc_start: 0.2469 (ttp) cc_final: 0.1394 (ppp) REVERT: I 1972 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8759 (pp) REVERT: I 2063 LEU cc_start: 0.6595 (mp) cc_final: 0.6278 (mm) REVERT: I 2068 MET cc_start: 0.6579 (mtm) cc_final: 0.6365 (mtt) REVERT: I 2185 MET cc_start: 0.4638 (mmm) cc_final: 0.4160 (tpp) REVERT: I 2189 MET cc_start: 0.4139 (mmm) cc_final: 0.3130 (ptm) REVERT: J 187 LEU cc_start: 0.5029 (OUTLIER) cc_final: 0.4800 (mt) REVERT: J 190 TYR cc_start: 0.3454 (t80) cc_final: 0.3033 (t80) REVERT: J 324 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6745 (pttm) REVERT: K 233 MET cc_start: 0.7936 (tpt) cc_final: 0.7707 (tpt) REVERT: K 269 ARG cc_start: 0.5046 (OUTLIER) cc_final: 0.4249 (mmm160) REVERT: L 36 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7748 (tm-30) REVERT: L 151 LYS cc_start: 0.6529 (ptmt) cc_final: 0.6216 (ptmt) REVERT: M 165 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7635 (mptt) REVERT: M 227 ASP cc_start: 0.8093 (t0) cc_final: 0.7588 (m-30) REVERT: M 388 GLU cc_start: 0.7615 (tp30) cc_final: 0.7412 (tp30) REVERT: M 408 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: N 62 MET cc_start: 0.8598 (ttp) cc_final: 0.8309 (ttp) REVERT: N 121 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7458 (mm-40) REVERT: N 276 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7503 (mp) REVERT: N 319 ASP cc_start: 0.7869 (m-30) cc_final: 0.7170 (t0) REVERT: N 379 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7475 (t0) REVERT: O 118 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7753 (ptp90) REVERT: O 237 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7922 (p0) REVERT: O 285 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6846 (mttp) REVERT: O 308 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: O 403 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7880 (tp) REVERT: O 455 MET cc_start: 0.8088 (mmm) cc_final: 0.7736 (mmm) REVERT: P 167 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7771 (pp20) REVERT: Q 264 MET cc_start: 0.4354 (mtp) cc_final: 0.4052 (mtp) REVERT: Q 343 ASP cc_start: 0.8556 (t0) cc_final: 0.8043 (m-30) REVERT: R 88 MET cc_start: 0.7834 (mmm) cc_final: 0.7559 (mmt) REVERT: R 207 ARG cc_start: 0.7669 (mpp-170) cc_final: 0.6919 (mpt180) REVERT: R 326 MET cc_start: 0.8924 (mtm) cc_final: 0.8495 (mtm) REVERT: S 121 GLN cc_start: 0.3132 (tt0) cc_final: 0.2450 (mt0) REVERT: S 123 MET cc_start: 0.3657 (mmt) cc_final: 0.2908 (ttt) REVERT: S 132 MET cc_start: 0.1748 (ptm) cc_final: 0.1049 (ptm) REVERT: T 282 MET cc_start: 0.0643 (ppp) cc_final: -0.2129 (mtt) REVERT: T 410 TRP cc_start: 0.0305 (m100) cc_final: -0.0047 (m100) REVERT: U 185 LEU cc_start: -0.0053 (OUTLIER) cc_final: -0.1004 (mt) REVERT: V 98 MET cc_start: 0.2803 (ptp) cc_final: 0.2560 (ptp) REVERT: V 119 GLU cc_start: -0.0395 (OUTLIER) cc_final: -0.1141 (tm-30) REVERT: W 29 ASN cc_start: 0.3370 (OUTLIER) cc_final: 0.2753 (t0) outliers start: 200 outliers final: 104 residues processed: 534 average time/residue: 0.5209 time to fit residues: 479.5422 Evaluate side-chains 451 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 328 time to evaluate : 4.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 990 VAL Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1914 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 306 THR Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 37 ASN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 385 ASN Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 126 SER Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 357 VAL Chi-restraints excluded: chain N residue 379 ASP Chi-restraints excluded: chain N residue 388 THR Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 206 CYS Chi-restraints excluded: chain O residue 237 ASP Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 308 ASP Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 269 LYS Chi-restraints excluded: chain P residue 324 LEU Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 419 THR Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 191 ILE Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 269 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 430 VAL Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain W residue 29 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 209 optimal weight: 8.9990 chunk 559 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 364 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 622 optimal weight: 10.0000 chunk 516 optimal weight: 0.2980 chunk 288 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 326 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2060 HIS ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN L 29 ASN M 203 GLN N 41 GLN O 316 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 233 GLN T 277 GLN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 296 ASN U 353 GLN W 29 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4829 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 57050 Z= 0.212 Angle : 0.602 13.591 78243 Z= 0.311 Chirality : 0.041 0.196 8827 Planarity : 0.004 0.085 9069 Dihedral : 20.080 171.185 10021 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.84 % Favored : 95.15 % Rotamer: Outliers : 2.67 % Allowed : 15.16 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 6201 helix: 1.05 (0.10), residues: 2922 sheet: -0.60 (0.17), residues: 811 loop : -1.10 (0.13), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 97 HIS 0.011 0.001 HIS S 88 PHE 0.034 0.002 PHE J 274 TYR 0.024 0.001 TYR J 326 ARG 0.007 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 353 time to evaluate : 4.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 614 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5203 (mm) REVERT: I 789 MET cc_start: 0.2437 (ttp) cc_final: 0.1389 (ppp) REVERT: I 886 HIS cc_start: 0.4669 (m90) cc_final: 0.4323 (m170) REVERT: I 917 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8838 (mp) REVERT: I 1972 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8631 (pp) REVERT: I 2063 LEU cc_start: 0.6884 (mp) cc_final: 0.6533 (mm) REVERT: I 2068 MET cc_start: 0.6423 (mtm) cc_final: 0.6210 (mtt) REVERT: I 2153 HIS cc_start: 0.1415 (m90) cc_final: 0.0475 (p-80) REVERT: I 2185 MET cc_start: 0.4647 (mmm) cc_final: 0.4294 (tpp) REVERT: I 2189 MET cc_start: 0.3664 (mmm) cc_final: 0.2572 (tmm) REVERT: J 190 TYR cc_start: 0.3788 (t80) cc_final: 0.3328 (t80) REVERT: K 1 MET cc_start: 0.6891 (tmm) cc_final: 0.6223 (tmm) REVERT: K 102 PHE cc_start: 0.3345 (m-10) cc_final: 0.3062 (m-10) REVERT: K 114 PHE cc_start: 0.7528 (m-80) cc_final: 0.7323 (m-80) REVERT: K 269 ARG cc_start: 0.4806 (OUTLIER) cc_final: 0.3673 (mmm-85) REVERT: L 36 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7670 (tm-30) REVERT: M 227 ASP cc_start: 0.7884 (t0) cc_final: 0.7340 (m-30) REVERT: M 371 MET cc_start: 0.8096 (mtp) cc_final: 0.7717 (ttm) REVERT: M 389 GLU cc_start: 0.7767 (tp30) cc_final: 0.7555 (tp30) REVERT: M 408 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: N 62 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8128 (ttp) REVERT: N 121 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7402 (mm-40) REVERT: N 319 ASP cc_start: 0.7932 (m-30) cc_final: 0.7498 (t0) REVERT: O 249 ARG cc_start: 0.7203 (ttm-80) cc_final: 0.6742 (ttm110) REVERT: O 285 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6809 (mttp) REVERT: O 362 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7539 (mtp180) REVERT: O 403 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7736 (tp) REVERT: O 455 MET cc_start: 0.7862 (mmm) cc_final: 0.7460 (mmm) REVERT: P 167 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7807 (pp20) REVERT: P 269 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7469 (tppt) REVERT: Q 113 MET cc_start: 0.6993 (tpt) cc_final: 0.6728 (tpt) REVERT: Q 343 ASP cc_start: 0.8550 (t0) cc_final: 0.7983 (m-30) REVERT: R 53 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8256 (mtm180) REVERT: R 90 MET cc_start: 0.8336 (mtp) cc_final: 0.7921 (mtp) REVERT: R 193 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7725 (tp) REVERT: R 274 GLU cc_start: 0.6796 (mp0) cc_final: 0.6495 (mp0) REVERT: R 326 MET cc_start: 0.8857 (mtm) cc_final: 0.8308 (mtm) REVERT: S 123 MET cc_start: 0.3668 (mmt) cc_final: 0.2890 (ttt) REVERT: S 132 MET cc_start: 0.1796 (ptm) cc_final: 0.1032 (ptm) REVERT: T 282 MET cc_start: 0.0490 (ppp) cc_final: -0.2197 (mtt) REVERT: T 410 TRP cc_start: 0.0142 (m100) cc_final: -0.0232 (m100) REVERT: U 185 LEU cc_start: -0.0147 (OUTLIER) cc_final: -0.1089 (mt) REVERT: V 119 GLU cc_start: -0.0156 (OUTLIER) cc_final: -0.1071 (tm-30) REVERT: V 253 LYS cc_start: 0.2489 (mttt) cc_final: 0.1661 (mmmt) REVERT: W 29 ASN cc_start: 0.2846 (OUTLIER) cc_final: 0.2574 (t0) outliers start: 144 outliers final: 81 residues processed: 469 average time/residue: 0.5100 time to fit residues: 413.1403 Evaluate side-chains 418 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 321 time to evaluate : 4.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 917 ILE Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1914 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 145 CYS Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 156 HIS Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 375 MET Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 397 ILE Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 206 CYS Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 285 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 148 ASP Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 310 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 322 MET Chi-restraints excluded: chain T residue 361 THR Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain W residue 29 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 599 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 354 optimal weight: 5.9990 chunk 454 optimal weight: 0.9990 chunk 352 optimal weight: 0.0270 chunk 523 optimal weight: 30.0000 chunk 347 optimal weight: 0.7980 chunk 619 optimal weight: 20.0000 chunk 387 optimal weight: 0.9990 chunk 377 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 902 ASN ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 241 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 GLN ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 353 GLN W 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4821 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 57050 Z= 0.194 Angle : 0.584 13.528 78243 Z= 0.301 Chirality : 0.041 0.334 8827 Planarity : 0.004 0.085 9069 Dihedral : 19.951 170.915 10019 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.90 % Favored : 95.08 % Rotamer: Outliers : 2.53 % Allowed : 15.55 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 6201 helix: 1.20 (0.10), residues: 2916 sheet: -0.56 (0.18), residues: 811 loop : -1.01 (0.13), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 97 HIS 0.012 0.001 HIS S 88 PHE 0.029 0.001 PHE J 274 TYR 0.026 0.001 TYR S 218 ARG 0.004 0.000 ARG I 866 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 337 time to evaluate : 4.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 ILE cc_start: 0.2346 (mm) cc_final: 0.1939 (mm) REVERT: H 84 MET cc_start: 0.4846 (ppp) cc_final: 0.4640 (ppp) REVERT: I 645 MET cc_start: 0.3937 (pmm) cc_final: 0.3217 (mmp) REVERT: I 684 MET cc_start: 0.2247 (tpt) cc_final: 0.2018 (tpp) REVERT: I 789 MET cc_start: 0.1626 (ttp) cc_final: 0.0628 (ppp) REVERT: I 931 ARG cc_start: 0.6999 (mmt-90) cc_final: 0.6758 (mpt180) REVERT: I 1972 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8632 (pp) REVERT: I 2063 LEU cc_start: 0.6865 (mp) cc_final: 0.6559 (mt) REVERT: I 2068 MET cc_start: 0.6517 (mtm) cc_final: 0.6270 (mtt) REVERT: I 2153 HIS cc_start: 0.1415 (m90) cc_final: 0.0513 (p-80) REVERT: I 2185 MET cc_start: 0.4648 (mmm) cc_final: 0.4301 (tpp) REVERT: I 2189 MET cc_start: 0.3581 (mmm) cc_final: 0.2493 (tmm) REVERT: J 190 TYR cc_start: 0.3844 (t80) cc_final: 0.3384 (t80) REVERT: K 1 MET cc_start: 0.7071 (tmm) cc_final: 0.6448 (tmm) REVERT: K 269 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.3629 (mmm-85) REVERT: M 165 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7902 (mmtp) REVERT: M 227 ASP cc_start: 0.7940 (t0) cc_final: 0.7352 (m-30) REVERT: M 371 MET cc_start: 0.8073 (mtp) cc_final: 0.7864 (ttm) REVERT: M 389 GLU cc_start: 0.7745 (tp30) cc_final: 0.7509 (tp30) REVERT: M 408 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7094 (mt0) REVERT: N 62 MET cc_start: 0.8384 (ttp) cc_final: 0.8093 (ttp) REVERT: N 121 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7436 (mm-40) REVERT: N 261 PHE cc_start: 0.8228 (p90) cc_final: 0.7859 (p90) REVERT: N 319 ASP cc_start: 0.7931 (m-30) cc_final: 0.7638 (t0) REVERT: O 113 MET cc_start: 0.7846 (tpt) cc_final: 0.7437 (tpp) REVERT: O 362 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7545 (mtp180) REVERT: O 403 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7624 (tp) REVERT: O 447 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7698 (mm) REVERT: O 455 MET cc_start: 0.7862 (mmm) cc_final: 0.7445 (mmm) REVERT: P 167 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7802 (pp20) REVERT: P 269 LYS cc_start: 0.7434 (mmtm) cc_final: 0.7217 (tppt) REVERT: P 305 ASP cc_start: 0.6072 (t0) cc_final: 0.5777 (t0) REVERT: Q 113 MET cc_start: 0.6971 (tpt) cc_final: 0.6701 (tpt) REVERT: Q 177 PHE cc_start: 0.6244 (t80) cc_final: 0.5955 (t80) REVERT: Q 343 ASP cc_start: 0.8570 (t0) cc_final: 0.7945 (m-30) REVERT: R 53 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8292 (mtm180) REVERT: R 90 MET cc_start: 0.8282 (mtp) cc_final: 0.8018 (mtp) REVERT: R 193 ILE cc_start: 0.7995 (tp) cc_final: 0.7697 (tp) REVERT: R 326 MET cc_start: 0.8793 (mtm) cc_final: 0.8172 (mtm) REVERT: S 123 MET cc_start: 0.3666 (mmt) cc_final: 0.2889 (ttt) REVERT: S 132 MET cc_start: 0.1798 (ptm) cc_final: 0.1037 (ptm) REVERT: T 282 MET cc_start: 0.0503 (ppp) cc_final: -0.2175 (mtt) REVERT: T 410 TRP cc_start: 0.0132 (m100) cc_final: -0.0222 (m100) REVERT: U 185 LEU cc_start: -0.0138 (OUTLIER) cc_final: -0.1062 (mt) REVERT: V 253 LYS cc_start: 0.3089 (mttt) cc_final: 0.2192 (mmmt) outliers start: 136 outliers final: 91 residues processed: 451 average time/residue: 0.5217 time to fit residues: 407.0764 Evaluate side-chains 422 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 320 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 136 HIS Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 992 MET Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2071 MET Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 145 CYS Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 165 LYS Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain O residue 403 LEU Chi-restraints excluded: chain O residue 447 LEU Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 269 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 310 SER Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 405 LEU Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 322 MET Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 383 optimal weight: 6.9990 chunk 247 optimal weight: 0.7980 chunk 370 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 394 optimal weight: 0.8980 chunk 422 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 487 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 HIS ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4825 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 57050 Z= 0.200 Angle : 0.585 16.988 78243 Z= 0.300 Chirality : 0.041 0.261 8827 Planarity : 0.004 0.085 9069 Dihedral : 19.862 170.179 10014 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.82 % Favored : 95.16 % Rotamer: Outliers : 2.47 % Allowed : 15.88 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.11), residues: 6201 helix: 1.25 (0.10), residues: 2923 sheet: -0.51 (0.18), residues: 808 loop : -0.97 (0.13), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 277 HIS 0.012 0.001 HIS S 88 PHE 0.025 0.001 PHE R 261 TYR 0.020 0.001 TYR S 218 ARG 0.005 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 347 time to evaluate : 4.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 84 MET cc_start: 0.4792 (ppp) cc_final: 0.4544 (ppp) REVERT: I 614 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5147 (mm) REVERT: I 645 MET cc_start: 0.3744 (pmm) cc_final: 0.2964 (mmp) REVERT: I 789 MET cc_start: 0.1365 (ttp) cc_final: 0.0069 (ppp) REVERT: I 864 ARG cc_start: 0.6523 (mmt-90) cc_final: 0.6125 (tpp80) REVERT: I 1972 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8590 (pp) REVERT: I 2063 LEU cc_start: 0.6840 (mp) cc_final: 0.6512 (mt) REVERT: I 2068 MET cc_start: 0.6482 (mtm) cc_final: 0.5825 (mtm) REVERT: I 2153 HIS cc_start: 0.1486 (m90) cc_final: 0.0480 (p-80) REVERT: I 2185 MET cc_start: 0.4699 (mmm) cc_final: 0.4337 (tpp) REVERT: I 2189 MET cc_start: 0.3622 (mmm) cc_final: 0.2394 (tmm) REVERT: J 190 TYR cc_start: 0.3838 (t80) cc_final: 0.3345 (t80) REVERT: K 1 MET cc_start: 0.7230 (tmm) cc_final: 0.6563 (tmm) REVERT: K 220 MET cc_start: 0.8816 (mmp) cc_final: 0.8584 (mmp) REVERT: K 269 ARG cc_start: 0.4524 (OUTLIER) cc_final: 0.3637 (mmm-85) REVERT: M 225 LYS cc_start: 0.8697 (ptmt) cc_final: 0.8362 (tptt) REVERT: M 227 ASP cc_start: 0.7984 (t0) cc_final: 0.7382 (m-30) REVERT: M 268 LYS cc_start: 0.6932 (ttpt) cc_final: 0.6637 (ttpt) REVERT: M 389 GLU cc_start: 0.7758 (tp30) cc_final: 0.7507 (tp30) REVERT: M 408 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7102 (mt0) REVERT: N 62 MET cc_start: 0.8347 (ttp) cc_final: 0.8040 (ttp) REVERT: N 121 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7452 (mm-40) REVERT: N 261 PHE cc_start: 0.8176 (p90) cc_final: 0.7798 (p90) REVERT: N 319 ASP cc_start: 0.7934 (m-30) cc_final: 0.7659 (t0) REVERT: O 113 MET cc_start: 0.7861 (tpt) cc_final: 0.7449 (tpp) REVERT: O 359 MET cc_start: 0.7277 (mtt) cc_final: 0.7069 (mtm) REVERT: O 362 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7546 (mtp180) REVERT: O 455 MET cc_start: 0.7901 (mmm) cc_final: 0.7339 (mmm) REVERT: P 167 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7842 (pp20) REVERT: Q 180 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8278 (mt) REVERT: Q 191 ILE cc_start: 0.8868 (mt) cc_final: 0.8585 (tt) REVERT: Q 274 LYS cc_start: 0.6984 (tmmt) cc_final: 0.6673 (tttp) REVERT: Q 343 ASP cc_start: 0.8506 (t0) cc_final: 0.7931 (m-30) REVERT: R 53 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8269 (mtm180) REVERT: R 193 ILE cc_start: 0.8088 (tp) cc_final: 0.7806 (tp) REVERT: R 274 GLU cc_start: 0.6869 (mp0) cc_final: 0.6537 (mp0) REVERT: R 326 MET cc_start: 0.8778 (mtm) cc_final: 0.8141 (mtm) REVERT: R 423 VAL cc_start: 0.8389 (p) cc_final: 0.8138 (t) REVERT: S 123 MET cc_start: 0.3655 (mmt) cc_final: 0.2702 (ttt) REVERT: S 132 MET cc_start: 0.1811 (ptm) cc_final: 0.1219 (ptm) REVERT: T 282 MET cc_start: -0.0030 (ppp) cc_final: -0.2243 (mtt) REVERT: T 410 TRP cc_start: 0.0000 (m100) cc_final: -0.0325 (m100) REVERT: U 185 LEU cc_start: -0.0120 (OUTLIER) cc_final: -0.1031 (mt) REVERT: V 253 LYS cc_start: 0.2986 (mttt) cc_final: 0.2499 (mmmt) REVERT: W 29 ASN cc_start: 0.3360 (OUTLIER) cc_final: 0.2871 (t0) outliers start: 133 outliers final: 98 residues processed: 453 average time/residue: 0.5038 time to fit residues: 394.4879 Evaluate side-chains 435 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 326 time to evaluate : 4.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 992 MET Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 145 CYS Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 375 MET Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 397 ILE Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 269 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 310 SER Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 405 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 322 MET Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain W residue 29 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 563 optimal weight: 8.9990 chunk 593 optimal weight: 7.9990 chunk 541 optimal weight: 4.9990 chunk 577 optimal weight: 10.0000 chunk 347 optimal weight: 0.6980 chunk 251 optimal weight: 6.9990 chunk 453 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 521 optimal weight: 30.0000 chunk 546 optimal weight: 5.9990 chunk 575 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN I 855 HIS I 902 ASN I2175 ASN ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN ** K 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN O 18 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 181 GLN R 447 GLN ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4928 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 57050 Z= 0.491 Angle : 0.750 14.360 78243 Z= 0.384 Chirality : 0.047 0.321 8827 Planarity : 0.006 0.091 9069 Dihedral : 20.069 167.308 10012 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 2.82 % Allowed : 15.88 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 6201 helix: 0.88 (0.10), residues: 2912 sheet: -0.62 (0.18), residues: 807 loop : -1.14 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 682 HIS 0.012 0.002 HIS S 88 PHE 0.026 0.002 PHE P 257 TYR 0.033 0.002 TYR P 446 ARG 0.012 0.001 ARG R 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 318 time to evaluate : 4.733 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: I 614 LEU cc_start: 0.5138 (OUTLIER) cc_final: 0.4775 (mm) REVERT: I 684 MET cc_start: 0.1938 (mmm) cc_final: 0.1505 (mmt) REVERT: I 789 MET cc_start: 0.1533 (ttp) cc_final: 0.0452 (ppp) REVERT: I 931 ARG cc_start: 0.6504 (mpt180) cc_final: 0.6182 (mpt180) REVERT: I 1972 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8735 (pp) REVERT: I 2063 LEU cc_start: 0.6734 (mp) cc_final: 0.6496 (mm) REVERT: I 2068 MET cc_start: 0.6508 (mtm) cc_final: 0.6019 (mtm) REVERT: I 2153 HIS cc_start: 0.1513 (m90) cc_final: 0.0476 (p-80) REVERT: I 2185 MET cc_start: 0.4499 (mmm) cc_final: 0.4110 (tpp) REVERT: I 2189 MET cc_start: 0.3351 (mmm) cc_final: 0.2188 (tmm) REVERT: J 173 LEU cc_start: 0.4756 (tp) cc_final: 0.4544 (tt) REVERT: J 190 TYR cc_start: 0.4142 (t80) cc_final: 0.3576 (t80) REVERT: K 1 MET cc_start: 0.7566 (tmm) cc_final: 0.6405 (tmm) REVERT: K 143 LEU cc_start: 0.8685 (mp) cc_final: 0.8441 (tt) REVERT: K 154 PHE cc_start: 0.1050 (OUTLIER) cc_final: 0.0246 (m-80) REVERT: K 269 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.4644 (mmm160) REVERT: M 227 ASP cc_start: 0.8242 (t0) cc_final: 0.7636 (m-30) REVERT: M 408 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: N 62 MET cc_start: 0.8370 (ttp) cc_final: 0.8030 (ttp) REVERT: N 121 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7495 (mm-40) REVERT: N 146 GLN cc_start: 0.8224 (mt0) cc_final: 0.7991 (mm-40) REVERT: O 15 ILE cc_start: 0.4946 (mp) cc_final: 0.4595 (mt) REVERT: O 455 MET cc_start: 0.8106 (mmm) cc_final: 0.7581 (tpp) REVERT: P 167 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7852 (pp20) REVERT: P 305 ASP cc_start: 0.6415 (t0) cc_final: 0.6076 (t70) REVERT: Q 180 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8379 (mm) REVERT: Q 213 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6956 (p90) REVERT: Q 274 LYS cc_start: 0.7030 (tmmt) cc_final: 0.6627 (tttp) REVERT: Q 343 ASP cc_start: 0.8557 (t0) cc_final: 0.8103 (m-30) REVERT: Q 376 LYS cc_start: 0.8947 (tptt) cc_final: 0.8628 (tppp) REVERT: R 20 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: R 90 MET cc_start: 0.8654 (mtp) cc_final: 0.8209 (mtp) REVERT: R 193 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7676 (tp) REVERT: R 326 MET cc_start: 0.8956 (mtm) cc_final: 0.8496 (mtm) REVERT: S 123 MET cc_start: 0.3917 (mmt) cc_final: 0.2818 (ttt) REVERT: S 132 MET cc_start: 0.1767 (ptm) cc_final: 0.1418 (ptm) REVERT: S 191 LYS cc_start: 0.2607 (tttt) cc_final: 0.2090 (tttt) REVERT: T 82 MET cc_start: 0.0255 (ttt) cc_final: -0.0053 (ttt) REVERT: T 222 MET cc_start: 0.1816 (ppp) cc_final: 0.1256 (ppp) REVERT: T 282 MET cc_start: -0.0137 (ppp) cc_final: -0.2204 (mtt) REVERT: T 410 TRP cc_start: 0.0072 (m100) cc_final: -0.0200 (m100) REVERT: U 185 LEU cc_start: 0.0046 (OUTLIER) cc_final: -0.1103 (mt) outliers start: 152 outliers final: 114 residues processed: 445 average time/residue: 0.5168 time to fit residues: 397.5075 Evaluate side-chains 431 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 305 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 992 MET Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 1991 HIS Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2116 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 301 TYR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 145 CYS Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 156 HIS Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 307 GLU Chi-restraints excluded: chain K residue 339 CYS Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 353 ASP Chi-restraints excluded: chain M residue 397 ILE Chi-restraints excluded: chain M residue 402 THR Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 325 ILE Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 257 LEU Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 378 GLU Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 269 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain R residue 35 ASP Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 320 MET Chi-restraints excluded: chain R residue 405 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 43 MET Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 322 MET Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 379 optimal weight: 0.7980 chunk 610 optimal weight: 7.9990 chunk 372 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 424 optimal weight: 1.9990 chunk 640 optimal weight: 20.0000 chunk 589 optimal weight: 20.0000 chunk 510 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 394 optimal weight: 0.9990 chunk 312 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 855 HIS I2175 ASN ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 HIS ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 GLN W 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4877 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 57050 Z= 0.252 Angle : 0.626 16.907 78243 Z= 0.322 Chirality : 0.042 0.260 8827 Planarity : 0.005 0.087 9069 Dihedral : 20.015 169.393 10012 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.87 % Rotamer: Outliers : 2.27 % Allowed : 16.33 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.11), residues: 6201 helix: 1.11 (0.10), residues: 2914 sheet: -0.56 (0.18), residues: 795 loop : -1.10 (0.13), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 250 HIS 0.012 0.001 HIS S 88 PHE 0.026 0.002 PHE R 261 TYR 0.022 0.001 TYR K 99 ARG 0.005 0.000 ARG M 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12402 Ramachandran restraints generated. 6201 Oldfield, 0 Emsley, 6201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 315 time to evaluate : 4.641 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: I 614 LEU cc_start: 0.4986 (OUTLIER) cc_final: 0.4637 (mm) REVERT: I 684 MET cc_start: 0.1782 (mmm) cc_final: 0.1421 (mmt) REVERT: I 789 MET cc_start: 0.1239 (ttp) cc_final: 0.0257 (ppp) REVERT: I 931 ARG cc_start: 0.6589 (mpt180) cc_final: 0.6341 (mpt180) REVERT: I 1972 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8649 (pp) REVERT: I 2063 LEU cc_start: 0.6688 (mp) cc_final: 0.6454 (mm) REVERT: I 2068 MET cc_start: 0.6392 (mtm) cc_final: 0.6014 (mtm) REVERT: I 2153 HIS cc_start: 0.1469 (m90) cc_final: 0.0579 (p-80) REVERT: I 2185 MET cc_start: 0.4570 (mmm) cc_final: 0.4177 (tpp) REVERT: I 2189 MET cc_start: 0.3365 (mmm) cc_final: 0.2181 (tmm) REVERT: J 182 LEU cc_start: 0.5484 (mt) cc_final: 0.4790 (pp) REVERT: J 324 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7241 (pttm) REVERT: K 1 MET cc_start: 0.7682 (tmm) cc_final: 0.6586 (tmm) REVERT: K 68 TRP cc_start: 0.8038 (m-90) cc_final: 0.7442 (m-90) REVERT: K 269 ARG cc_start: 0.5132 (OUTLIER) cc_final: 0.4085 (mmm-85) REVERT: K 394 PHE cc_start: 0.6237 (t80) cc_final: 0.5950 (t80) REVERT: M 225 LYS cc_start: 0.8695 (ptmt) cc_final: 0.8376 (tptt) REVERT: M 227 ASP cc_start: 0.8140 (t0) cc_final: 0.7475 (m-30) REVERT: M 268 LYS cc_start: 0.6835 (ttpt) cc_final: 0.6604 (ttpt) REVERT: M 408 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7112 (mt0) REVERT: N 62 MET cc_start: 0.8345 (ttp) cc_final: 0.7998 (ttp) REVERT: N 121 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7420 (mm-40) REVERT: N 261 PHE cc_start: 0.8023 (p90) cc_final: 0.7598 (p90) REVERT: O 15 ILE cc_start: 0.4609 (mp) cc_final: 0.4279 (mt) REVERT: O 61 MET cc_start: 0.8623 (tpp) cc_final: 0.8399 (mmm) REVERT: O 455 MET cc_start: 0.7894 (mmm) cc_final: 0.7305 (tpp) REVERT: P 167 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7897 (pp20) REVERT: P 305 ASP cc_start: 0.6137 (t0) cc_final: 0.5799 (t0) REVERT: Q 113 MET cc_start: 0.6939 (tpt) cc_final: 0.6676 (tpt) REVERT: Q 213 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.7095 (p90) REVERT: Q 274 LYS cc_start: 0.6958 (tmmt) cc_final: 0.6550 (tttm) REVERT: Q 343 ASP cc_start: 0.8506 (t0) cc_final: 0.8086 (m-30) REVERT: R 90 MET cc_start: 0.8310 (mtp) cc_final: 0.7945 (mtp) REVERT: R 132 LYS cc_start: 0.7525 (ptpt) cc_final: 0.7121 (pptt) REVERT: R 193 ILE cc_start: 0.7903 (tp) cc_final: 0.7655 (tp) REVERT: R 274 GLU cc_start: 0.6607 (mp0) cc_final: 0.6232 (mp0) REVERT: R 326 MET cc_start: 0.8895 (mtm) cc_final: 0.8309 (mtm) REVERT: S 123 MET cc_start: 0.3887 (mmt) cc_final: 0.2822 (ttt) REVERT: S 132 MET cc_start: 0.1668 (ptm) cc_final: 0.1215 (ptm) REVERT: S 191 LYS cc_start: 0.2502 (tttt) cc_final: 0.2047 (tptt) REVERT: T 222 MET cc_start: 0.1838 (ppp) cc_final: 0.1494 (ppp) REVERT: T 254 MET cc_start: 0.1653 (mmt) cc_final: 0.1358 (mmt) REVERT: T 282 MET cc_start: -0.0320 (ppp) cc_final: -0.2343 (mtt) REVERT: U 185 LEU cc_start: -0.0001 (OUTLIER) cc_final: -0.1143 (mt) outliers start: 122 outliers final: 99 residues processed: 416 average time/residue: 0.5197 time to fit residues: 373.5498 Evaluate side-chains 413 residues out of total 5403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 305 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 936 HIS Chi-restraints excluded: chain I residue 992 MET Chi-restraints excluded: chain I residue 1901 LEU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1972 ILE Chi-restraints excluded: chain I residue 1991 HIS Chi-restraints excluded: chain I residue 2069 THR Chi-restraints excluded: chain I residue 2085 LEU Chi-restraints excluded: chain I residue 2134 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 324 LYS Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 145 CYS Chi-restraints excluded: chain K residue 146 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 351 LEU Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 316 HIS Chi-restraints excluded: chain M residue 397 ILE Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain N residue 121 GLN Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 231 GLU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 260 MET Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 167 GLU Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 365 LYS Chi-restraints excluded: chain P residue 378 GLU Chi-restraints excluded: chain P residue 426 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 213 PHE Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 269 THR Chi-restraints excluded: chain Q residue 272 THR Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 255 GLN Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 43 MET Chi-restraints excluded: chain T residue 80 GLU Chi-restraints excluded: chain T residue 322 MET Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain U residue 56 ASP Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 282 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain V residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 405 optimal weight: 5.9990 chunk 543 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 chunk 470 optimal weight: 40.0000 chunk 75 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 510 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 524 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 855 HIS ** I2084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2126 ASN I2175 ASN ** K 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 429 HIS ** M 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 441 GLN O 18 HIS ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 429 HIS ** P 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.159482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.104788 restraints weight = 145569.973| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 5.11 r_work: 0.3289 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.6682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.138 57050 Z= 0.630 Angle : 0.850 17.389 78243 Z= 0.434 Chirality : 0.051 0.386 8827 Planarity : 0.007 0.107 9069 Dihedral : 20.271 166.682 10011 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.50 % Favored : 93.44 % Rotamer: Outliers : 2.58 % Allowed : 16.20 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 6201 helix: 0.60 (0.09), residues: 2926 sheet: -0.70 (0.18), residues: 799 loop : -1.42 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP T 250 HIS 0.012 0.002 HIS S 88 PHE 0.037 0.003 PHE I 923 TYR 0.033 0.003 TYR P 446 ARG 0.013 0.001 ARG R 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12803.70 seconds wall clock time: 224 minutes 38.27 seconds (13478.27 seconds total)