Starting phenix.real_space_refine on Tue Sep 24 12:53:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wif_37565/09_2024/8wif_37565.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wif_37565/09_2024/8wif_37565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wif_37565/09_2024/8wif_37565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wif_37565/09_2024/8wif_37565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wif_37565/09_2024/8wif_37565.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wif_37565/09_2024/8wif_37565.cif" } resolution = 2.9 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 1517 5.49 5 S 42 5.16 5 C 27126 2.51 5 N 9902 2.21 5 O 14196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 52783 Number of models: 1 Model: "" Number of chains: 23 Chain: "a" Number of atoms: 32561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1517, 32561 Classifications: {'RNA': 1517} Modifications used: {'rna2p_pur': 111, 'rna2p_pyr': 85, 'rna3p_pur': 739, 'rna3p_pyr': 582} Link IDs: {'rna2p': 196, 'rna3p': 1320} Chain: "v" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 271 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "d" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1656 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "e" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "f" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1236 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "g" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "h" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1207 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "i" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "j" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "k" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 784 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "l" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 855 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "m" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "n" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "o" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 819 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "p" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "q" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "r" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "s" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 513 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "t" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 662 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "u" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "c" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "x" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "w" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 23.12, per 1000 atoms: 0.44 Number of scatterers: 52783 At special positions: 0 Unit cell: (218.28, 205.44, 186.18, 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 42 16.00 P 1517 15.00 O 14196 8.00 N 9902 7.00 C 27126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.33 Conformation dependent library (CDL) restraints added in 2.5 seconds 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4720 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 24 sheets defined 45.8% alpha, 19.4% beta 519 base pairs and 812 stacking pairs defined. Time for finding SS restraints: 19.11 Creating SS restraints... Processing helix chain 'v' and resid 3 through 24 removed outlier: 4.512A pdb=" N LYS v 7 " --> pdb=" O SER v 3 " (cutoff:3.500A) Processing helix chain 'v' and resid 24 through 32 Processing helix chain 'd' and resid 6 through 11 Processing helix chain 'd' and resid 27 through 46 Processing helix chain 'd' and resid 71 through 76 removed outlier: 3.764A pdb=" N VAL d 75 " --> pdb=" O ARG d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 92 Processing helix chain 'd' and resid 107 through 110 Processing helix chain 'd' and resid 111 through 126 removed outlier: 3.653A pdb=" N ASN d 125 " --> pdb=" O GLU d 121 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG d 126 " --> pdb=" O GLN d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 142 Processing helix chain 'd' and resid 156 through 160 Processing helix chain 'e' and resid 8 through 16 removed outlier: 3.588A pdb=" N SER e 12 " --> pdb=" O ALA e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 29 removed outlier: 3.676A pdb=" N GLU e 27 " --> pdb=" O ASP e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 60 Processing helix chain 'e' and resid 63 through 77 Processing helix chain 'e' and resid 80 through 91 Processing helix chain 'e' and resid 92 through 100 Processing helix chain 'e' and resid 105 through 115 Processing helix chain 'e' and resid 142 through 145 Processing helix chain 'e' and resid 147 through 155 Processing helix chain 'e' and resid 182 through 187 removed outlier: 4.593A pdb=" N ASP e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 200 removed outlier: 3.937A pdb=" N ILE e 195 " --> pdb=" O THR e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 80 through 95 Processing helix chain 'f' and resid 133 through 144 Processing helix chain 'f' and resid 157 through 170 Processing helix chain 'f' and resid 174 through 183 Processing helix chain 'f' and resid 185 through 190 removed outlier: 3.502A pdb=" N VAL f 189 " --> pdb=" O PRO f 185 " (cutoff:3.500A) Processing helix chain 'f' and resid 191 through 204 removed outlier: 3.510A pdb=" N LEU f 195 " --> pdb=" O PRO f 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 15 through 17 No H-bonds generated for 'chain 'g' and resid 15 through 17' Processing helix chain 'g' and resid 18 through 27 Processing helix chain 'g' and resid 27 through 35 removed outlier: 3.932A pdb=" N GLY g 34 " --> pdb=" O ILE g 30 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY g 35 " --> pdb=" O ARG g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 82 Processing helix chain 'h' and resid 20 through 31 removed outlier: 3.916A pdb=" N THR h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 55 Processing helix chain 'h' and resid 57 through 70 removed outlier: 3.902A pdb=" N THR h 61 " --> pdb=" O ASP h 57 " (cutoff:3.500A) Processing helix chain 'h' and resid 92 through 110 Processing helix chain 'h' and resid 115 through 129 Processing helix chain 'h' and resid 132 through 148 Processing helix chain 'h' and resid 149 through 154 removed outlier: 4.317A pdb=" N HIS h 153 " --> pdb=" O ALA h 150 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR h 154 " --> pdb=" O PHE h 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 20 Processing helix chain 'i' and resid 30 through 43 Processing helix chain 'i' and resid 97 through 101 Processing helix chain 'i' and resid 115 through 122 Processing helix chain 'j' and resid 61 through 76 Proline residue: j 71 - end of helix Processing helix chain 'j' and resid 91 through 111 Processing helix chain 'j' and resid 114 through 122 removed outlier: 3.520A pdb=" N ALA j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 32 Processing helix chain 'k' and resid 80 through 88 Processing helix chain 'l' and resid 57 through 60 removed outlier: 3.812A pdb=" N GLY l 60 " --> pdb=" O GLY l 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 57 through 60' Processing helix chain 'l' and resid 62 through 67 Processing helix chain 'l' and resid 68 through 85 Processing helix chain 'l' and resid 101 through 112 Processing helix chain 'm' and resid 3 through 11 Processing helix chain 'm' and resid 113 through 117 Processing helix chain 'n' and resid 14 through 21 removed outlier: 3.848A pdb=" N TYR n 21 " --> pdb=" O ILE n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 26 through 38 removed outlier: 3.895A pdb=" N SER n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 64 Processing helix chain 'n' and resid 66 through 84 removed outlier: 3.701A pdb=" N LEU n 70 " --> pdb=" O VAL n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 94 Processing helix chain 'n' and resid 107 through 112 Processing helix chain 'o' and resid 3 through 21 removed outlier: 3.516A pdb=" N GLU o 11 " --> pdb=" O ILE o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 33 removed outlier: 3.788A pdb=" N LYS o 28 " --> pdb=" O ARG o 24 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 38 through 43 removed outlier: 3.734A pdb=" N ALA o 42 " --> pdb=" O PRO o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 43 through 51 removed outlier: 3.607A pdb=" N LEU o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 60 Proline residue: o 57 - end of helix Processing helix chain 'o' and resid 81 through 90 Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 46 removed outlier: 3.808A pdb=" N VAL p 45 " --> pdb=" O GLU p 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 74 removed outlier: 3.501A pdb=" N GLY p 55 " --> pdb=" O HIS p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 74 through 86 Processing helix chain 'q' and resid 52 through 63 Processing helix chain 'q' and resid 67 through 77 Processing helix chain 'q' and resid 78 through 85 Processing helix chain 'q' and resid 101 through 114 Processing helix chain 's' and resid 34 through 40 removed outlier: 3.760A pdb=" N LEU s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 50 through 55 Processing helix chain 's' and resid 57 through 74 Processing helix chain 't' and resid 12 through 24 Processing helix chain 't' and resid 41 through 45 removed outlier: 3.992A pdb=" N ILE t 45 " --> pdb=" O PRO t 42 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 75 Processing helix chain 'u' and resid 4 through 42 Processing helix chain 'u' and resid 44 through 64 Processing helix chain 'u' and resid 68 through 86 Processing helix chain 'c' and resid 7 through 13 Processing helix chain 'c' and resid 24 through 28 Processing helix chain 'c' and resid 42 through 63 removed outlier: 3.818A pdb=" N THR c 46 " --> pdb=" O ASP c 42 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS c 52 " --> pdb=" O THR c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 76 Processing helix chain 'c' and resid 77 through 88 Processing helix chain 'c' and resid 103 through 124 removed outlier: 3.708A pdb=" N LYS c 109 " --> pdb=" O SER c 105 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG c 110 " --> pdb=" O THR c 106 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU c 111 " --> pdb=" O VAL c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 148 Processing helix chain 'c' and resid 169 through 180 removed outlier: 3.677A pdb=" N VAL c 173 " --> pdb=" O GLU c 169 " (cutoff:3.500A) Processing helix chain 'c' and resid 206 through 227 Processing helix chain 'x' and resid 57 through 65 Processing helix chain 'w' and resid 13 through 24 removed outlier: 3.800A pdb=" N ARG w 24 " --> pdb=" O GLU w 20 " (cutoff:3.500A) Processing helix chain 'w' and resid 73 through 93 Processing helix chain 'w' and resid 95 through 100 Processing sheet with id=AA1, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.635A pdb=" N ASP d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 164 through 171 removed outlier: 3.715A pdb=" N LYS d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP d 181 " --> pdb=" O LYS d 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 49 removed outlier: 5.466A pdb=" N GLU f 38 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLY f 65 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL f 40 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE f 63 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER f 42 " --> pdb=" O LEU f 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 101 through 102 removed outlier: 3.557A pdb=" N THR f 105 " --> pdb=" O ILE f 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 110 through 114 removed outlier: 6.101A pdb=" N ILE f 131 " --> pdb=" O ALA f 150 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER f 152 " --> pdb=" O ILE f 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 37 through 47 removed outlier: 3.688A pdb=" N VAL g 37 " --> pdb=" O LYS g 66 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR g 60 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY g 58 " --> pdb=" O ARG g 45 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG g 92 " --> pdb=" O PRO g 3 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU g 5 " --> pdb=" O VAL g 90 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL g 90 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET g 7 " --> pdb=" O THR g 88 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR g 88 " --> pdb=" O MET g 7 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE g 9 " --> pdb=" O LEU g 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 73 through 79 Processing sheet with id=AA9, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.699A pdb=" N ASP i 48 " --> pdb=" O GLN i 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'i' and resid 76 through 79 Processing sheet with id=AB2, first strand: chain 'i' and resid 76 through 79 removed outlier: 5.966A pdb=" N VAL i 127 " --> pdb=" O SER i 107 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER i 107 " --> pdb=" O VAL i 127 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA i 129 " --> pdb=" O ILE i 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'j' and resid 27 through 32 Processing sheet with id=AB4, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.022A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS k 11 " --> pdb=" O ASP k 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.022A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'l' and resid 49 through 55 removed outlier: 6.973A pdb=" N ILE l 43 " --> pdb=" O ILE l 51 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP l 53 " --> pdb=" O VAL l 41 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL l 41 " --> pdb=" O TRP l 53 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER l 55 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR l 39 " --> pdb=" O SER l 55 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL l 91 " --> pdb=" O GLY l 117 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE l 119 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL l 93 " --> pdb=" O ILE l 119 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP l 121 " --> pdb=" O VAL l 93 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL l 95 " --> pdb=" O ASP l 121 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 29 through 40 removed outlier: 6.495A pdb=" N ARG m 54 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL m 37 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL m 52 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR m 39 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG m 50 " --> pdb=" O THR m 39 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR m 95 " --> pdb=" O THR m 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 3 through 4 Processing sheet with id=AB9, first strand: chain 'o' and resid 73 through 74 removed outlier: 3.581A pdb=" N LEU o 79 " --> pdb=" O LEU o 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'q' and resid 49 through 51 removed outlier: 6.028A pdb=" N ILE q 20 " --> pdb=" O ILE q 37 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG q 39 " --> pdb=" O TYR q 18 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR q 18 " --> pdb=" O ARG q 39 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL q 3 " --> pdb=" O GLN q 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'r' and resid 22 through 32 removed outlier: 15.978A pdb=" N THR r 22 " --> pdb=" O ARG r 43 " (cutoff:3.500A) removed outlier: 12.290A pdb=" N ARG r 43 " --> pdb=" O THR r 22 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE r 24 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU r 41 " --> pdb=" O ILE r 24 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL r 37 " --> pdb=" O VAL r 28 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP r 30 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR r 35 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 16.423A pdb=" N LYS r 86 " --> pdb=" O THR r 56 " (cutoff:3.500A) removed outlier: 13.635A pdb=" N LYS r 58 " --> pdb=" O LYS r 86 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N TRP r 88 " --> pdb=" O LYS r 58 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS r 60 " --> pdb=" O TRP r 88 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU r 90 " --> pdb=" O LYS r 60 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS r 62 " --> pdb=" O LEU r 90 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N GLU r 92 " --> pdb=" O HIS r 62 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ARG r 87 " --> pdb=" O THR r 79 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER r 75 " --> pdb=" O VAL r 91 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILE r 93 " --> pdb=" O ARG r 73 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG r 73 " --> pdb=" O ILE r 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 't' and resid 31 through 32 removed outlier: 6.954A pdb=" N ILE t 31 " --> pdb=" O ALA t 50 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N HIS t 52 " --> pdb=" O ILE t 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 31 through 35 Processing sheet with id=AC5, first strand: chain 'c' and resid 91 through 92 removed outlier: 8.570A pdb=" N VAL c 92 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE c 69 " --> pdb=" O VAL c 92 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL c 161 " --> pdb=" O ILE c 184 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE c 186 " --> pdb=" O VAL c 161 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL c 163 " --> pdb=" O ILE c 186 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR c 198 " --> pdb=" O VAL c 183 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA c 185 " --> pdb=" O TYR c 198 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'w' and resid 4 through 6 removed outlier: 3.610A pdb=" N LEU w 40 " --> pdb=" O SER w 6 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP w 59 " --> pdb=" O LEU w 34 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA w 36 " --> pdb=" O ASN w 57 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN w 57 " --> pdb=" O ALA w 36 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL w 38 " --> pdb=" O GLN w 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN w 55 " --> pdb=" O VAL w 38 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU w 40 " --> pdb=" O ILE w 53 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE w 53 " --> pdb=" O LEU w 40 " (cutoff:3.500A) 1027 hydrogen bonds defined for protein. 2931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1323 hydrogen bonds 2044 hydrogen bond angles 0 basepair planarities 519 basepair parallelities 812 stacking parallelities Total time for adding SS restraints: 36.99 Time building geometry restraints manager: 11.47 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: 8259 1.33 - 1.45: 22616 1.45 - 1.57: 22990 1.57 - 1.69: 3033 1.69 - 1.81: 74 Bond restraints: 56972 Sorted by residual: bond pdb=" C ASP o 33 " pdb=" N PRO o 34 " ideal model delta sigma weight residual 1.335 1.351 -0.016 8.70e-03 1.32e+04 3.42e+00 bond pdb=" CG1 ILE n 17 " pdb=" CD1 ILE n 17 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.35e+00 bond pdb=" CB GLN j 47 " pdb=" CG GLN j 47 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" CB VAL m 107 " pdb=" CG2 VAL m 107 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.70e+00 bond pdb=" C3' C a1149 " pdb=" O3' C a1149 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.50e-02 4.44e+03 1.70e+00 ... (remaining 56967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 83606 2.40 - 4.81: 767 4.81 - 7.21: 78 7.21 - 9.61: 10 9.61 - 12.02: 3 Bond angle restraints: 84464 Sorted by residual: angle pdb=" C GLN l 84 " pdb=" N GLU l 85 " pdb=" CA GLU l 85 " ideal model delta sigma weight residual 121.18 112.68 8.50 1.98e+00 2.55e-01 1.84e+01 angle pdb=" C SER u 48 " pdb=" N GLU u 49 " pdb=" CA GLU u 49 " ideal model delta sigma weight residual 121.14 114.17 6.97 1.75e+00 3.27e-01 1.59e+01 angle pdb=" CA GLU r 39 " pdb=" CB GLU r 39 " pdb=" CG GLU r 39 " ideal model delta sigma weight residual 114.10 122.03 -7.93 2.00e+00 2.50e-01 1.57e+01 angle pdb=" C3' U a 429 " pdb=" O3' U a 429 " pdb=" P A a 430 " ideal model delta sigma weight residual 120.20 126.00 -5.80 1.50e+00 4.44e-01 1.50e+01 angle pdb=" C3' C a1149 " pdb=" O3' C a1149 " pdb=" P A a1150 " ideal model delta sigma weight residual 120.20 125.69 -5.49 1.50e+00 4.44e-01 1.34e+01 ... (remaining 84459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 32241 35.55 - 71.10: 4055 71.10 - 106.65: 445 106.65 - 142.21: 14 142.21 - 177.76: 22 Dihedral angle restraints: 36777 sinusoidal: 29455 harmonic: 7322 Sorted by residual: dihedral pdb=" O4' U a 200 " pdb=" C1' U a 200 " pdb=" N1 U a 200 " pdb=" C2 U a 200 " ideal model delta sinusoidal sigma weight residual 200.00 33.42 166.58 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U a 328 " pdb=" C1' U a 328 " pdb=" N1 U a 328 " pdb=" C2 U a 328 " ideal model delta sinusoidal sigma weight residual -160.00 4.29 -164.29 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' C a 415 " pdb=" C1' C a 415 " pdb=" N1 C a 415 " pdb=" C2 C a 415 " ideal model delta sinusoidal sigma weight residual -160.00 1.22 -161.22 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 36774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 9581 0.062 - 0.123: 968 0.123 - 0.185: 90 0.185 - 0.246: 17 0.246 - 0.308: 4 Chirality restraints: 10660 Sorted by residual: chirality pdb=" C3' U a1482 " pdb=" C4' U a1482 " pdb=" O3' U a1482 " pdb=" C2' U a1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3' A a 895 " pdb=" C4' A a 895 " pdb=" O3' A a 895 " pdb=" C2' A a 895 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C1' U a1206 " pdb=" O4' U a1206 " pdb=" C2' U a1206 " pdb=" N1 U a1206 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 10657 not shown) Planarity restraints: 5103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A a1339 " -0.037 2.00e-02 2.50e+03 1.71e-02 8.01e+00 pdb=" N9 A a1339 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A a1339 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A a1339 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A a1339 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A a1339 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A a1339 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A a1339 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A a1339 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A a1339 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A a1339 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A a 940 " 0.037 2.00e-02 2.50e+03 1.68e-02 7.81e+00 pdb=" N9 A a 940 " -0.039 2.00e-02 2.50e+03 pdb=" C8 A a 940 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A a 940 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A a 940 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A a 940 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A a 940 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A a 940 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A a 940 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A a 940 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A a 940 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP e 126 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" CG ASP e 126 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP e 126 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP e 126 " 0.016 2.00e-02 2.50e+03 ... (remaining 5100 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1348 2.63 - 3.19: 42920 3.19 - 3.76: 105057 3.76 - 4.33: 141650 4.33 - 4.90: 193425 Nonbonded interactions: 484400 Sorted by model distance: nonbonded pdb=" O2' U a 438 " pdb=" O2 U a 439 " model vdw 2.057 3.040 nonbonded pdb=" O2 U a 83 " pdb=" O6 G a 86 " model vdw 2.074 2.432 nonbonded pdb=" O2' A a 772 " pdb=" N7 A a 774 " model vdw 2.081 3.120 nonbonded pdb=" OP1 C a 669 " pdb=" OG SER l 55 " model vdw 2.099 3.040 nonbonded pdb=" O ILE g 30 " pdb=" OG1 THR g 36 " model vdw 2.112 3.040 ... (remaining 484395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.750 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 117.070 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.140 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:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 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 : 0.006 0.071 56972 Z= 0.374 Angle : 0.625 12.017 84464 Z= 0.325 Chirality : 0.039 0.308 10660 Planarity : 0.005 0.063 5103 Dihedral : 23.741 177.758 32057 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 4.98 % Allowed : 33.08 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.79 (0.17), residues: 2513 helix: 1.64 (0.16), residues: 1039 sheet: 0.35 (0.26), residues: 439 loop : -0.50 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP t 34 HIS 0.006 0.001 HIS c 15 PHE 0.014 0.002 PHE d 129 TYR 0.023 0.002 TYR s 41 ARG 0.013 0.001 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 260 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: t 27 THR cc_start: 0.8261 (t) cc_final: 0.8006 (p) REVERT: t 34 TRP cc_start: 0.9057 (OUTLIER) cc_final: 0.8758 (m-10) outliers start: 106 outliers final: 86 residues processed: 348 average time/residue: 1.2242 time to fit residues: 550.9730 Evaluate side-chains 334 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 247 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 206 ASP Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 99 ARG Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 101 LEU Chi-restraints excluded: chain f residue 152 SER Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 36 ILE Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 131 VAL Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 148 SER Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 37 ASN Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 59 SER Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 49 THR Chi-restraints excluded: chain o residue 16 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 53 SER Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain t residue 24 GLU Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain c residue 80 ILE Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 336 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 311 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 361 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 GLN e 75 ASN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 47 GLN l 84 GLN ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS c 142 ASN c 167 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 56972 Z= 0.285 Angle : 0.590 9.967 84464 Z= 0.307 Chirality : 0.038 0.288 10660 Planarity : 0.005 0.050 5103 Dihedral : 23.808 179.531 27025 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 5.50 % Allowed : 29.61 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.84 (0.17), residues: 2513 helix: 1.74 (0.16), residues: 1064 sheet: 0.31 (0.25), residues: 444 loop : -0.59 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP w 96 HIS 0.005 0.001 HIS w 30 PHE 0.018 0.002 PHE x 61 TYR 0.013 0.001 TYR j 58 ARG 0.006 0.000 ARG k 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 274 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 207 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8758 (mt) REVERT: e 111 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: g 32 LYS cc_start: 0.9274 (pptt) cc_final: 0.8970 (ptpp) REVERT: k 14 ASP cc_start: 0.7918 (t0) cc_final: 0.7712 (t0) REVERT: l 45 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7824 (p0) REVERT: m 36 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8283 (ttp80) REVERT: n 80 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8127 (tmm-80) REVERT: u 7 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8842 (mm-40) REVERT: c 154 MET cc_start: 0.6961 (mmm) cc_final: 0.6179 (mmm) REVERT: c 187 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6767 (pp) outliers start: 117 outliers final: 58 residues processed: 363 average time/residue: 1.3500 time to fit residues: 624.2731 Evaluate side-chains 313 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 248 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 36 ILE Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 104 ASP Chi-restraints excluded: chain r residue 33 GLN Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 7 GLN Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain c residue 80 ILE Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 187 LEU Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 200 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 300 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 362 optimal weight: 10.0000 chunk 391 optimal weight: 6.9990 chunk 322 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 290 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN e 185 GLN ** k 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS c 94 GLN c 142 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 56972 Z= 0.329 Angle : 0.602 9.541 84464 Z= 0.312 Chirality : 0.038 0.298 10660 Planarity : 0.005 0.050 5103 Dihedral : 23.725 178.455 26949 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 7.05 % Allowed : 28.90 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.80 (0.17), residues: 2513 helix: 1.70 (0.16), residues: 1075 sheet: 0.27 (0.25), residues: 445 loop : -0.61 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP w 96 HIS 0.004 0.001 HIS w 30 PHE 0.016 0.002 PHE c 104 TYR 0.015 0.002 TYR c 198 ARG 0.007 0.000 ARG s 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 265 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 53 ASP cc_start: 0.7614 (t0) cc_final: 0.7392 (t0) REVERT: d 207 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8762 (mt) REVERT: e 111 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.8523 (tm-30) REVERT: e 133 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8664 (p) REVERT: e 136 ASP cc_start: 0.8488 (m-30) cc_final: 0.8145 (m-30) REVERT: g 64 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: h 66 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9147 (mm) REVERT: k 14 ASP cc_start: 0.8003 (t0) cc_final: 0.7795 (t0) REVERT: l 45 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7922 (p0) REVERT: n 12 ASP cc_start: 0.8106 (t0) cc_final: 0.7870 (t0) REVERT: n 65 LYS cc_start: 0.8909 (ptmm) cc_final: 0.8630 (ptmm) REVERT: n 80 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8152 (tmm-80) REVERT: n 102 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9118 (ptp-170) REVERT: r 55 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9198 (p) REVERT: u 7 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8836 (mm-40) REVERT: c 59 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: c 154 MET cc_start: 0.6933 (mmm) cc_final: 0.6093 (mmm) outliers start: 150 outliers final: 75 residues processed: 374 average time/residue: 1.3086 time to fit residues: 623.4135 Evaluate side-chains 343 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 257 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 133 MET Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 36 ILE Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 149 LYS Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 46 LYS Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 18 GLN Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 104 ASP Chi-restraints excluded: chain r residue 33 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 25 LYS Chi-restraints excluded: chain t residue 27 THR Chi-restraints excluded: chain t residue 39 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 7 GLN Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 80 ILE Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 66 ARG Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 357 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 243 optimal weight: 7.9990 chunk 363 optimal weight: 3.9990 chunk 384 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS c 142 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 56972 Z= 0.340 Angle : 0.608 9.711 84464 Z= 0.315 Chirality : 0.039 0.300 10660 Planarity : 0.005 0.058 5103 Dihedral : 23.706 177.662 26942 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 6.95 % Allowed : 29.37 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.79 (0.17), residues: 2513 helix: 1.70 (0.16), residues: 1075 sheet: 0.21 (0.25), residues: 448 loop : -0.61 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.004 0.001 HIS p 18 PHE 0.018 0.002 PHE x 61 TYR 0.017 0.002 TYR d 31 ARG 0.005 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 280 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 53 ASP cc_start: 0.7601 (t0) cc_final: 0.7271 (t0) REVERT: d 82 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: d 133 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8543 (mtp) REVERT: d 207 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8779 (mt) REVERT: e 111 GLN cc_start: 0.9411 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: e 133 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8540 (p) REVERT: e 136 ASP cc_start: 0.8521 (m-30) cc_final: 0.8046 (m-30) REVERT: f 77 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7694 (ptmt) REVERT: g 74 GLU cc_start: 0.8638 (tp30) cc_final: 0.8419 (tp30) REVERT: h 66 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9167 (mm) REVERT: j 34 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: j 55 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9101 (tt) REVERT: k 14 ASP cc_start: 0.8027 (t0) cc_final: 0.7797 (t0) REVERT: l 107 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8277 (mtp180) REVERT: m 36 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8302 (ttp80) REVERT: n 65 LYS cc_start: 0.8915 (ptmm) cc_final: 0.8623 (ptmm) REVERT: n 102 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.9109 (ptp-170) REVERT: n 108 ARG cc_start: 0.9483 (OUTLIER) cc_final: 0.8131 (mmm160) REVERT: o 32 ARG cc_start: 0.6478 (mtp180) cc_final: 0.6213 (mtp180) REVERT: r 55 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.9226 (p) REVERT: u 7 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8842 (mm-40) REVERT: c 59 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: c 154 MET cc_start: 0.7116 (mmm) cc_final: 0.6285 (mmm) outliers start: 148 outliers final: 77 residues processed: 391 average time/residue: 1.3824 time to fit residues: 683.1441 Evaluate side-chains 348 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 255 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 133 MET Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 36 ILE Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 149 LYS Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 16 LEU Chi-restraints excluded: chain o residue 18 GLN Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 104 ASP Chi-restraints excluded: chain r residue 33 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 25 LYS Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 7 GLN Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 80 ILE Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 66 ARG Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 320 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 345 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 57 HIS c 15 HIS ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 56972 Z= 0.295 Angle : 0.597 9.387 84464 Z= 0.310 Chirality : 0.038 0.291 10660 Planarity : 0.005 0.050 5103 Dihedral : 23.699 177.633 26937 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 6.39 % Allowed : 30.22 % Favored : 63.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.87 (0.17), residues: 2513 helix: 1.80 (0.16), residues: 1073 sheet: 0.20 (0.25), residues: 451 loop : -0.56 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.004 0.001 HIS c 15 PHE 0.014 0.002 PHE c 104 TYR 0.018 0.001 TYR c 198 ARG 0.010 0.000 ARG s 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 272 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 53 ASP cc_start: 0.7595 (t0) cc_final: 0.7166 (t0) REVERT: d 82 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: d 107 ASN cc_start: 0.8235 (m110) cc_final: 0.8003 (m110) REVERT: d 133 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8584 (mtp) REVERT: d 207 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8774 (mt) REVERT: e 111 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.8565 (tm-30) REVERT: e 133 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8529 (p) REVERT: e 136 ASP cc_start: 0.8584 (m-30) cc_final: 0.8046 (m-30) REVERT: f 77 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7723 (ptmt) REVERT: g 43 TRP cc_start: 0.8354 (OUTLIER) cc_final: 0.7597 (p-90) REVERT: g 74 GLU cc_start: 0.8573 (tp30) cc_final: 0.8311 (tp30) REVERT: h 66 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9170 (mm) REVERT: j 34 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: k 14 ASP cc_start: 0.8035 (t0) cc_final: 0.7796 (t0) REVERT: l 107 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8278 (mtp180) REVERT: m 36 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8298 (ttp80) REVERT: n 65 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8620 (ptmm) REVERT: n 102 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.9071 (ptp-170) REVERT: n 108 ARG cc_start: 0.9483 (OUTLIER) cc_final: 0.8156 (mmm160) REVERT: o 23 ARG cc_start: 0.8126 (pmm150) cc_final: 0.7528 (tpp-160) REVERT: o 32 ARG cc_start: 0.6480 (mtp180) cc_final: 0.6208 (mtp180) REVERT: p 14 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7720 (tm-30) REVERT: q 107 ASN cc_start: 0.9350 (m110) cc_final: 0.8867 (m-40) REVERT: r 55 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9222 (p) REVERT: u 7 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8811 (mm-40) REVERT: c 27 MET cc_start: 0.7094 (mmm) cc_final: 0.6810 (mtm) REVERT: c 59 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: c 154 MET cc_start: 0.7233 (mmm) cc_final: 0.6338 (mmm) outliers start: 136 outliers final: 82 residues processed: 370 average time/residue: 1.3672 time to fit residues: 641.5383 Evaluate side-chains 356 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 258 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 133 MET Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 36 ILE Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 149 LYS Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain k residue 46 LYS Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 16 LEU Chi-restraints excluded: chain o residue 18 GLN Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 33 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 7 GLN Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 66 ARG Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 129 optimal weight: 10.0000 chunk 346 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 385 optimal weight: 7.9990 chunk 319 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 56972 Z= 0.290 Angle : 0.596 12.238 84464 Z= 0.308 Chirality : 0.037 0.291 10660 Planarity : 0.005 0.055 5103 Dihedral : 23.682 177.547 26934 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 6.25 % Allowed : 30.92 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.17), residues: 2513 helix: 1.77 (0.16), residues: 1079 sheet: 0.23 (0.25), residues: 450 loop : -0.58 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.005 0.001 HIS c 15 PHE 0.018 0.002 PHE x 61 TYR 0.018 0.001 TYR d 31 ARG 0.008 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 272 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 53 ASP cc_start: 0.7597 (t0) cc_final: 0.7127 (t0) REVERT: d 107 ASN cc_start: 0.8234 (m110) cc_final: 0.8004 (m110) REVERT: d 187 TYR cc_start: 0.8802 (t80) cc_final: 0.8598 (t80) REVERT: d 207 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8814 (mt) REVERT: e 111 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: e 133 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8531 (p) REVERT: e 136 ASP cc_start: 0.8574 (m-30) cc_final: 0.8015 (m-30) REVERT: f 77 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7730 (ptmt) REVERT: g 43 TRP cc_start: 0.8333 (OUTLIER) cc_final: 0.7601 (p-90) REVERT: g 74 GLU cc_start: 0.8575 (tp30) cc_final: 0.8241 (tp30) REVERT: h 66 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9190 (mm) REVERT: j 34 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: k 14 ASP cc_start: 0.8046 (t0) cc_final: 0.7784 (t0) REVERT: l 107 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8277 (mtp180) REVERT: l 137 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8468 (ptt90) REVERT: m 36 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8298 (ttp80) REVERT: n 65 LYS cc_start: 0.8931 (ptmm) cc_final: 0.8625 (ptmm) REVERT: n 102 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.9055 (ptp-170) REVERT: n 108 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.8186 (mmm160) REVERT: o 32 ARG cc_start: 0.6460 (mtp180) cc_final: 0.6160 (mtp180) REVERT: p 89 ARG cc_start: 0.5189 (OUTLIER) cc_final: 0.4931 (ptt90) REVERT: r 55 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9203 (p) REVERT: u 7 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8804 (mm-40) REVERT: c 27 MET cc_start: 0.7298 (mmm) cc_final: 0.7025 (mtm) REVERT: c 59 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: c 154 MET cc_start: 0.7155 (mmm) cc_final: 0.6274 (mmm) outliers start: 133 outliers final: 83 residues processed: 373 average time/residue: 1.4009 time to fit residues: 658.6080 Evaluate side-chains 359 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 260 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 GLU Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 149 LYS Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 137 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 115 SER Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 16 LEU Chi-restraints excluded: chain o residue 18 GLN Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 89 ARG Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 33 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 7 GLN Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 66 ARG Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 371 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 chunk 281 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 383 optimal weight: 20.0000 chunk 240 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS c 142 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 56972 Z= 0.274 Angle : 0.593 10.765 84464 Z= 0.307 Chirality : 0.037 0.287 10660 Planarity : 0.004 0.050 5103 Dihedral : 23.672 177.484 26931 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 6.16 % Allowed : 31.25 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.17), residues: 2513 helix: 1.80 (0.16), residues: 1079 sheet: 0.26 (0.25), residues: 445 loop : -0.58 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.005 0.001 HIS c 15 PHE 0.012 0.001 PHE c 104 TYR 0.018 0.001 TYR d 31 ARG 0.009 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 273 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 53 ASP cc_start: 0.7621 (t0) cc_final: 0.7128 (t0) REVERT: d 133 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7217 (mpt) REVERT: d 187 TYR cc_start: 0.8831 (t80) cc_final: 0.8497 (t80) REVERT: d 207 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8802 (mt) REVERT: e 111 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.8536 (tm-30) REVERT: e 133 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8557 (p) REVERT: e 136 ASP cc_start: 0.8546 (m-30) cc_final: 0.8065 (m-30) REVERT: f 77 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7907 (ptmt) REVERT: g 43 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7732 (p-90) REVERT: g 74 GLU cc_start: 0.8547 (tp30) cc_final: 0.8188 (tp30) REVERT: j 34 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: k 14 ASP cc_start: 0.8069 (t0) cc_final: 0.7762 (t0) REVERT: l 107 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8275 (mtp180) REVERT: l 137 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8483 (ptt90) REVERT: m 36 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8298 (ttp80) REVERT: n 51 ASP cc_start: 0.8430 (p0) cc_final: 0.8046 (p0) REVERT: n 65 LYS cc_start: 0.8937 (ptmm) cc_final: 0.8620 (ptmm) REVERT: n 80 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8157 (tmm-80) REVERT: n 102 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.9036 (ptp-170) REVERT: n 108 ARG cc_start: 0.9485 (OUTLIER) cc_final: 0.8175 (mmm160) REVERT: o 32 ARG cc_start: 0.6438 (mtp180) cc_final: 0.6124 (mtp180) REVERT: p 14 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7721 (tm-30) REVERT: p 89 ARG cc_start: 0.5220 (OUTLIER) cc_final: 0.4957 (ptt90) REVERT: q 107 ASN cc_start: 0.9348 (m110) cc_final: 0.8894 (m-40) REVERT: r 55 THR cc_start: 0.9436 (OUTLIER) cc_final: 0.9233 (p) REVERT: u 7 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8786 (mm-40) REVERT: c 59 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: c 154 MET cc_start: 0.7397 (mmm) cc_final: 0.6540 (mmm) REVERT: c 162 TRP cc_start: 0.7195 (OUTLIER) cc_final: 0.6712 (t-100) outliers start: 131 outliers final: 82 residues processed: 373 average time/residue: 1.4098 time to fit residues: 661.3622 Evaluate side-chains 364 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 264 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 GLU Chi-restraints excluded: chain d residue 133 MET Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 36 ILE Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 149 LYS Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain l residue 137 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 115 SER Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 16 LEU Chi-restraints excluded: chain o residue 18 GLN Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 89 ARG Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 33 GLN Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 77 MET Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 7 GLN Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 162 TRP Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 66 ARG Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 237 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 243 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 301 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 GLN ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS c 142 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 56972 Z= 0.203 Angle : 0.584 10.628 84464 Z= 0.303 Chirality : 0.035 0.277 10660 Planarity : 0.005 0.060 5103 Dihedral : 23.700 177.722 26931 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 5.64 % Allowed : 31.63 % Favored : 62.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.90 (0.17), residues: 2513 helix: 1.82 (0.16), residues: 1079 sheet: 0.34 (0.25), residues: 439 loop : -0.61 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.005 0.001 HIS c 15 PHE 0.018 0.001 PHE x 61 TYR 0.019 0.001 TYR d 31 ARG 0.019 0.000 ARG s 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 270 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 53 ASP cc_start: 0.7595 (t0) cc_final: 0.7117 (t0) REVERT: d 133 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7210 (mpt) REVERT: d 187 TYR cc_start: 0.8816 (t80) cc_final: 0.8524 (t80) REVERT: d 207 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8798 (mt) REVERT: e 111 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: e 133 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8567 (p) REVERT: e 136 ASP cc_start: 0.8593 (m-30) cc_final: 0.8144 (m-30) REVERT: f 77 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7917 (ptmt) REVERT: f 176 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: g 43 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.7713 (p-90) REVERT: g 64 ASP cc_start: 0.8248 (m-30) cc_final: 0.7992 (m-30) REVERT: g 74 GLU cc_start: 0.8527 (tp30) cc_final: 0.8162 (tp30) REVERT: j 34 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: k 14 ASP cc_start: 0.8099 (t0) cc_final: 0.7825 (t0) REVERT: m 36 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8287 (ttp80) REVERT: n 65 LYS cc_start: 0.8934 (ptmm) cc_final: 0.8629 (ptmm) REVERT: n 80 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8127 (tmm-80) REVERT: n 102 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.9014 (ptp-170) REVERT: n 108 ARG cc_start: 0.9475 (OUTLIER) cc_final: 0.8202 (mmm160) REVERT: o 32 ARG cc_start: 0.6431 (mtp180) cc_final: 0.6180 (mtp180) REVERT: p 14 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7738 (tm-30) REVERT: p 89 ARG cc_start: 0.5191 (OUTLIER) cc_final: 0.4933 (ptt90) REVERT: q 45 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7882 (tp30) REVERT: q 107 ASN cc_start: 0.9348 (m110) cc_final: 0.8889 (m-40) REVERT: r 55 THR cc_start: 0.9424 (OUTLIER) cc_final: 0.9217 (p) REVERT: s 44 GLU cc_start: 0.7735 (pm20) cc_final: 0.7117 (pm20) REVERT: s 45 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.7996 (tpp-160) REVERT: c 59 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: c 154 MET cc_start: 0.7406 (mmm) cc_final: 0.6518 (mmm) outliers start: 120 outliers final: 80 residues processed: 359 average time/residue: 1.3667 time to fit residues: 621.5519 Evaluate side-chains 357 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 262 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 GLU Chi-restraints excluded: chain d residue 133 MET Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain f residue 176 GLU Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 36 ILE Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 149 LYS Chi-restraints excluded: chain k residue 10 LEU Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 115 SER Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 16 LEU Chi-restraints excluded: chain o residue 18 GLN Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 89 ARG Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 66 ARG Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 348 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 335 optimal weight: 5.9990 chunk 357 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 323 optimal weight: 7.9990 chunk 338 optimal weight: 7.9990 chunk 356 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS c 142 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 56972 Z= 0.297 Angle : 0.610 10.340 84464 Z= 0.315 Chirality : 0.038 0.294 10660 Planarity : 0.005 0.057 5103 Dihedral : 23.656 177.306 26931 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 5.26 % Allowed : 32.24 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.87 (0.17), residues: 2513 helix: 1.77 (0.16), residues: 1078 sheet: 0.34 (0.26), residues: 442 loop : -0.62 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.006 0.001 HIS c 15 PHE 0.012 0.002 PHE c 104 TYR 0.019 0.001 TYR d 31 ARG 0.011 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 267 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 53 ASP cc_start: 0.7620 (t0) cc_final: 0.7116 (t0) REVERT: d 107 ASN cc_start: 0.8235 (m110) cc_final: 0.7998 (m110) REVERT: d 133 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7231 (mpt) REVERT: d 187 TYR cc_start: 0.8875 (t80) cc_final: 0.8577 (t80) REVERT: d 207 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8794 (mt) REVERT: e 111 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: e 133 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8443 (p) REVERT: e 136 ASP cc_start: 0.8541 (m-30) cc_final: 0.8059 (m-30) REVERT: f 77 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7914 (ptmt) REVERT: g 43 TRP cc_start: 0.8360 (OUTLIER) cc_final: 0.7734 (p-90) REVERT: g 74 GLU cc_start: 0.8532 (tp30) cc_final: 0.8150 (tp30) REVERT: j 34 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: k 14 ASP cc_start: 0.8135 (t0) cc_final: 0.7835 (t0) REVERT: l 107 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8281 (mtp180) REVERT: m 36 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8303 (ttp80) REVERT: n 65 LYS cc_start: 0.8940 (ptmm) cc_final: 0.8622 (ptmm) REVERT: n 102 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.9054 (ptp-170) REVERT: n 108 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.8176 (mmm160) REVERT: o 32 ARG cc_start: 0.6426 (mtp180) cc_final: 0.6161 (mtp180) REVERT: p 14 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7908 (tm-30) REVERT: p 89 ARG cc_start: 0.5298 (OUTLIER) cc_final: 0.5037 (ptt90) REVERT: q 107 ASN cc_start: 0.9347 (m110) cc_final: 0.8888 (m-40) REVERT: r 55 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9232 (p) REVERT: s 44 GLU cc_start: 0.7690 (pm20) cc_final: 0.7012 (pm20) REVERT: s 45 ARG cc_start: 0.8321 (tpp-160) cc_final: 0.7966 (tpp-160) REVERT: c 59 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: c 154 MET cc_start: 0.7468 (mmm) cc_final: 0.6607 (mmm) outliers start: 112 outliers final: 81 residues processed: 357 average time/residue: 1.3634 time to fit residues: 614.9598 Evaluate side-chains 354 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 259 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 GLU Chi-restraints excluded: chain d residue 133 MET Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 36 ILE Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 149 LYS Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 115 SER Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 16 LEU Chi-restraints excluded: chain o residue 18 GLN Chi-restraints excluded: chain o residue 41 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 89 ARG Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 104 ASP Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 27 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 66 ARG Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 234 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 396 optimal weight: 7.9990 chunk 364 optimal weight: 30.0000 chunk 315 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 56972 Z= 0.297 Angle : 0.612 10.096 84464 Z= 0.316 Chirality : 0.038 0.293 10660 Planarity : 0.005 0.061 5103 Dihedral : 23.658 177.237 26930 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 4.70 % Allowed : 32.61 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.88 (0.17), residues: 2513 helix: 1.78 (0.16), residues: 1073 sheet: 0.34 (0.25), residues: 448 loop : -0.60 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.007 0.001 HIS c 15 PHE 0.015 0.002 PHE x 61 TYR 0.020 0.001 TYR d 31 ARG 0.012 0.000 ARG l 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5026 Ramachandran restraints generated. 2513 Oldfield, 0 Emsley, 2513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 271 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 53 ASP cc_start: 0.7621 (t0) cc_final: 0.7085 (t0) REVERT: d 107 ASN cc_start: 0.8240 (m110) cc_final: 0.8005 (m110) REVERT: d 124 SER cc_start: 0.9162 (p) cc_final: 0.8958 (t) REVERT: d 133 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7231 (mpt) REVERT: d 187 TYR cc_start: 0.8886 (t80) cc_final: 0.8591 (t80) REVERT: d 207 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8794 (mt) REVERT: e 111 GLN cc_start: 0.9413 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: e 133 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8431 (p) REVERT: e 136 ASP cc_start: 0.8552 (m-30) cc_final: 0.8082 (m-30) REVERT: f 77 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7911 (ptmt) REVERT: g 43 TRP cc_start: 0.8358 (OUTLIER) cc_final: 0.7731 (p-90) REVERT: g 74 GLU cc_start: 0.8530 (tp30) cc_final: 0.8147 (tp30) REVERT: j 34 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: k 14 ASP cc_start: 0.8137 (t0) cc_final: 0.7841 (t0) REVERT: m 36 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8303 (ttp80) REVERT: n 51 ASP cc_start: 0.8407 (p0) cc_final: 0.8043 (p0) REVERT: n 65 LYS cc_start: 0.8931 (ptmm) cc_final: 0.8611 (ptmm) REVERT: n 102 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.9049 (ptp-170) REVERT: n 108 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.8174 (mmm160) REVERT: o 32 ARG cc_start: 0.6419 (mtp180) cc_final: 0.6160 (mtp180) REVERT: o 54 ASP cc_start: 0.8941 (m-30) cc_final: 0.8730 (t70) REVERT: p 89 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.4712 (ptt90) REVERT: q 107 ASN cc_start: 0.9353 (m110) cc_final: 0.8877 (m-40) REVERT: s 44 GLU cc_start: 0.7620 (pm20) cc_final: 0.6934 (pm20) REVERT: s 45 ARG cc_start: 0.8340 (tpp-160) cc_final: 0.7973 (tpp-160) REVERT: c 59 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: c 154 MET cc_start: 0.7495 (mmm) cc_final: 0.6621 (mmm) outliers start: 100 outliers final: 78 residues processed: 353 average time/residue: 1.3959 time to fit residues: 621.1983 Evaluate side-chains 354 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 264 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 GLU Chi-restraints excluded: chain d residue 133 MET Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 44 SER Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 77 LYS Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain f residue 173 GLN Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 85 TYR Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 36 ILE Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 81 SER Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain j residue 149 LYS Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 26 VAL Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain l residue 110 GLN Chi-restraints excluded: chain l residue 118 THR Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 115 SER Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 45 THR Chi-restraints excluded: chain n residue 80 ARG Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain n residue 108 ARG Chi-restraints excluded: chain o residue 16 LEU Chi-restraints excluded: chain o residue 18 GLN Chi-restraints excluded: chain o residue 41 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 89 ARG Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 104 ASP Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 27 THR Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain c residue 163 VAL Chi-restraints excluded: chain w residue 27 ARG Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 66 ARG Chi-restraints excluded: chain w residue 84 ARG Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 250 optimal weight: 5.9990 chunk 336 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 324 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 ASN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 HIS ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.040742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.030710 restraints weight = 316594.673| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.63 r_work: 0.2670 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 56972 Z= 0.286 Angle : 0.614 11.227 84464 Z= 0.317 Chirality : 0.037 0.290 10660 Planarity : 0.005 0.060 5103 Dihedral : 23.656 177.237 26928 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 4.89 % Allowed : 32.57 % Favored : 62.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.87 (0.17), residues: 2513 helix: 1.75 (0.16), residues: 1076 sheet: 0.33 (0.25), residues: 450 loop : -0.58 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.007 0.001 HIS c 15 PHE 0.012 0.001 PHE c 104 TYR 0.020 0.001 TYR d 31 ARG 0.012 0.000 ARG l 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11842.49 seconds wall clock time: 205 minutes 54.22 seconds (12354.22 seconds total)