Starting phenix.real_space_refine on Sat Dec 28 13:21:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wi9_37561/12_2024/8wi9_37561.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wi9_37561/12_2024/8wi9_37561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wi9_37561/12_2024/8wi9_37561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wi9_37561/12_2024/8wi9_37561.map" model { file = "/net/cci-nas-00/data/ceres_data/8wi9_37561/12_2024/8wi9_37561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wi9_37561/12_2024/8wi9_37561.cif" } resolution = 3.5 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 1515 5.49 5 S 50 5.16 5 C 28236 2.51 5 N 10153 2.21 5 O 14505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 54459 Number of models: 1 Model: "" Number of chains: 24 Chain: "a" Number of atoms: 32521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32521 Classifications: {'RNA': 1515} Modifications used: {'rna2p_pur': 111, 'rna2p_pyr': 85, 'rna3p_pur': 739, 'rna3p_pyr': 580} Link IDs: {'rna2p': 196, 'rna3p': 1318} Chain: "b" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1193 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 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: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1223 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} 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: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain breaks: 2 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: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} 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: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} 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: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2030 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 20, 'TRANS': 234} Time building chain proxies: 23.02, per 1000 atoms: 0.42 Number of scatterers: 54459 At special positions: 0 Unit cell: (211.86, 206.51, 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 50 16.00 P 1515 15.00 O 14505 8.00 N 10153 7.00 C 28236 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: 9.92 Conformation dependent library (CDL) restraints added in 2.7 seconds 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5122 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 29 sheets defined 43.0% alpha, 20.9% beta 521 base pairs and 769 stacking pairs defined. Time for finding SS restraints: 20.90 Creating SS restraints... Processing helix chain 'b' and resid 18 through 30 removed outlier: 3.686A pdb=" N ILE b 30 " --> pdb=" O ILE b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 80 Processing helix chain 'b' and resid 104 through 118 Processing helix chain 'b' and resid 151 through 153 No H-bonds generated for 'chain 'b' and resid 151 through 153' Processing helix chain 'v' and resid 4 through 32 removed outlier: 5.393A pdb=" N VAL v 26 " --> pdb=" O ARG v 22 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN v 27 " --> pdb=" O ARG v 23 " (cutoff:3.500A) 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: 3.726A 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 111 through 126 removed outlier: 3.967A pdb=" N ASN d 125 " --> pdb=" O GLU d 121 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG d 126 " --> pdb=" O GLN d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 143 removed outlier: 3.698A pdb=" N ARG d 142 " --> pdb=" O GLN d 138 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN d 143 " --> pdb=" O SER d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 160 removed outlier: 3.558A pdb=" N ALA d 160 " --> pdb=" O LEU d 157 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 16 Processing helix chain 'e' and resid 24 through 29 Processing helix chain 'e' and resid 44 through 60 removed outlier: 3.642A pdb=" N TYR e 60 " --> pdb=" O ALA e 56 " (cutoff:3.500A) 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 removed outlier: 3.544A pdb=" N LEU e 145 " --> pdb=" O GLU e 142 " (cutoff:3.500A) No H-bonds generated for '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: 4.825A pdb=" N ASP e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 200 removed outlier: 4.000A 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 171 Processing helix chain 'f' and resid 174 through 183 Processing helix chain 'f' and resid 185 through 190 Processing helix chain 'f' and resid 191 through 202 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 35 removed outlier: 4.367A pdb=" N VAL g 29 " --> pdb=" O THR g 25 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE g 30 " --> pdb=" O PHE g 26 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY g 34 " --> pdb=" O ILE g 30 " (cutoff:3.500A) removed outlier: 3.942A 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: 3.852A 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: 3.668A pdb=" N THR h 61 " --> pdb=" O ASP h 57 " (cutoff:3.500A) Processing helix chain 'h' and resid 92 through 110 removed outlier: 3.548A pdb=" N GLN h 110 " --> pdb=" O ASN h 106 " (cutoff:3.500A) 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: 4.347A pdb=" N HIS h 153 " --> pdb=" O ALA h 150 " (cutoff:3.500A) removed outlier: 3.867A 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 Processing helix chain 'k' and resid 14 through 30 Processing helix chain 'l' and resid 57 through 60 removed outlier: 3.739A 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 removed outlier: 3.612A pdb=" N ARG l 65 " --> pdb=" O LYS l 62 " (cutoff:3.500A) 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 21 through 25 Processing helix chain 'm' and resid 113 through 118 removed outlier: 3.750A pdb=" N GLY m 118 " --> pdb=" O SER m 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 20 Processing helix chain 'n' and resid 27 through 38 Processing helix chain 'n' and resid 44 through 48 removed outlier: 3.532A pdb=" N ASP n 47 " --> pdb=" O ARG n 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU n 48 " --> pdb=" O THR n 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 44 through 48' Processing helix chain 'n' and resid 49 through 64 Processing helix chain 'n' and resid 67 through 84 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 11 removed outlier: 3.911A pdb=" N ASN o 11 " --> pdb=" O VAL o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 20 removed outlier: 3.886A pdb=" N ARG o 19 " --> pdb=" O PHE o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 40 through 51 Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 44 Processing helix chain 'p' and resid 49 through 74 Processing helix chain 'p' and resid 74 through 86 Processing helix chain 'q' and resid 52 through 62 Processing helix chain 'q' and resid 67 through 78 Processing helix chain 'q' and resid 78 through 85 Processing helix chain 'q' and resid 101 through 114 removed outlier: 3.609A pdb=" N GLU q 114 " --> pdb=" O LEU q 110 " (cutoff:3.500A) Processing helix chain 's' and resid 34 through 40 removed outlier: 3.776A 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: 3.664A 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 43 through 64 removed outlier: 3.994A pdb=" N ALA u 47 " --> pdb=" O ASP u 43 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 86 Processing helix chain 'c' and resid 7 through 13 removed outlier: 3.858A pdb=" N SER c 12 " --> pdb=" O GLN c 8 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY c 13 " --> pdb=" O LEU c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 29 removed outlier: 4.375A pdb=" N ARG c 29 " --> pdb=" O LYS c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 63 removed outlier: 3.880A pdb=" N THR c 46 " --> pdb=" O ASP c 42 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS c 52 " --> pdb=" O THR c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 75 No H-bonds generated for 'chain 'c' and resid 73 through 75' Processing helix chain 'c' and resid 76 through 88 removed outlier: 3.807A pdb=" N ILE c 80 " --> pdb=" O ALA c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 124 removed outlier: 3.936A pdb=" N LYS c 109 " --> pdb=" O SER c 105 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG c 110 " --> pdb=" O THR c 106 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 148 Processing helix chain 'c' and resid 150 through 154 removed outlier: 4.028A pdb=" N ASP c 153 " --> pdb=" O GLY c 150 " (cutoff:3.500A) Processing helix chain 'c' and resid 169 through 180 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 23 Processing helix chain 'w' and resid 24 through 26 No H-bonds generated for 'chain 'w' and resid 24 through 26' Processing helix chain 'w' and resid 73 through 93 Processing helix chain 'w' and resid 95 through 100 Processing helix chain 'w' and resid 145 through 157 removed outlier: 3.718A pdb=" N LEU w 156 " --> pdb=" O GLU w 152 " (cutoff:3.500A) Processing helix chain 'w' and resid 178 through 180 No H-bonds generated for 'chain 'w' and resid 178 through 180' Processing helix chain 'w' and resid 213 through 225 Processing sheet with id=AA1, first strand: chain 'b' and resid 38 through 42 removed outlier: 6.794A pdb=" N ILE b 101 " --> pdb=" O LEU b 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 50 through 53 Processing sheet with id=AA3, first strand: chain 'b' and resid 168 through 169 removed outlier: 3.753A pdb=" N GLY b 128 " --> pdb=" O ILE b 169 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR b 129 " --> pdb=" O ASP b 141 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE b 139 " --> pdb=" O ILE b 131 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG b 145 " --> pdb=" O VAL b 183 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU b 185 " --> pdb=" O ARG b 145 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE b 147 " --> pdb=" O LEU b 185 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL b 184 " --> pdb=" O ILE b 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.582A pdb=" N ARG d 58 " --> pdb=" O ARG d 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL d 63 " --> pdb=" O GLN d 99 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASN d 101 " --> pdb=" O VAL d 63 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL d 65 " --> pdb=" O ASN d 101 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU d 103 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE d 67 " --> pdb=" O LEU d 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 164 through 171 removed outlier: 3.936A pdb=" N LYS d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASP d 181 " --> pdb=" O LYS d 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 123 through 124 Processing sheet with id=AA7, first strand: chain 'f' and resid 37 through 49 removed outlier: 5.339A pdb=" N GLU f 38 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY f 65 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL f 40 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE f 63 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER f 42 " --> pdb=" O LEU f 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 101 through 102 removed outlier: 3.551A pdb=" N THR f 105 " --> pdb=" O ILE f 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 110 through 114 removed outlier: 6.399A pdb=" N ILE f 131 " --> pdb=" O ALA f 150 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N SER f 152 " --> pdb=" O ILE f 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 37 through 42 removed outlier: 3.789A pdb=" N VAL g 37 " --> pdb=" O LYS g 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 37 through 42 removed outlier: 3.789A pdb=" N VAL g 37 " --> pdb=" O LYS g 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 73 through 79 Processing sheet with id=AB4, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.671A pdb=" N ASP i 48 " --> pdb=" O GLN i 63 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 76 through 79 Processing sheet with id=AB6, first strand: chain 'i' and resid 76 through 79 removed outlier: 6.931A pdb=" N ILE i 105 " --> pdb=" O LEU i 128 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR i 130 " --> pdb=" O VAL i 103 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL i 103 " --> pdb=" O TYR i 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 27 through 32 removed outlier: 6.689A pdb=" N ASN j 49 " --> pdb=" O ALA j 85 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU j 87 " --> pdb=" O ASN j 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'k' and resid 40 through 52 removed outlier: 5.877A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS k 11 " --> pdb=" O ASP k 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'k' and resid 40 through 52 removed outlier: 5.877A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 49 through 55 removed outlier: 5.583A pdb=" N VAL l 50 " --> pdb=" O ASP l 45 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP l 45 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA l 52 " --> pdb=" O ILE l 43 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY l 28 " --> pdb=" O ASP l 92 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N PHE l 94 " --> pdb=" O GLY l 28 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA l 30 " --> pdb=" O PHE l 94 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LYS l 96 " --> pdb=" O ALA l 30 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE l 32 " --> pdb=" O LYS l 96 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL l 91 " --> pdb=" O GLY l 117 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE l 119 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL l 93 " --> pdb=" O ILE l 119 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP l 121 " --> pdb=" O VAL l 93 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL l 95 " --> pdb=" O ASP l 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 29 through 40 removed outlier: 5.971A pdb=" N CYS m 34 " --> pdb=" O LYS m 56 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS m 56 " --> pdb=" O CYS m 34 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N TYR m 95 " --> pdb=" O GLU m 62 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR m 64 " --> pdb=" O TYR m 95 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE m 97 " --> pdb=" O THR m 64 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR m 66 " --> pdb=" O ILE m 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'n' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'q' and resid 49 through 51 removed outlier: 5.965A pdb=" N VAL q 36 " --> pdb=" O VAL q 22 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL q 22 " --> pdb=" O VAL q 36 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL q 3 " --> pdb=" O GLN q 65 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'r' and resid 22 through 32 removed outlier: 15.914A pdb=" N THR r 22 " --> pdb=" O ARG r 43 " (cutoff:3.500A) removed outlier: 12.292A pdb=" N ARG r 43 " --> pdb=" O THR r 22 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE r 24 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU r 41 " --> pdb=" O ILE r 24 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL r 37 " --> pdb=" O VAL r 28 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP r 30 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR r 35 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N LYS r 86 " --> pdb=" O LYS r 58 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LYS r 60 " --> pdb=" O LYS r 86 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU r 90 " --> pdb=" O HIS r 62 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG r 87 " --> pdb=" O PRO r 81 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG r 89 " --> pdb=" O THR r 79 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR r 79 " --> pdb=" O ARG r 89 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL r 91 " --> pdb=" O MET r 77 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N MET r 77 " --> pdb=" O VAL r 91 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE r 93 " --> pdb=" O SER r 75 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER r 75 " --> pdb=" O ILE r 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 't' and resid 31 through 33 removed outlier: 7.099A pdb=" N ILE t 31 " --> pdb=" O ALA t 50 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N HIS t 52 " --> pdb=" O ILE t 31 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N THR t 33 " --> pdb=" O HIS t 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 16 through 19 removed outlier: 5.916A pdb=" N PHE c 16 " --> pdb=" O ILE c 41 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE c 41 " --> pdb=" O PHE c 16 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS c 18 " --> pdb=" O TYR c 39 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE c 38 " --> pdb=" O ASP c 34 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP c 34 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE c 40 " --> pdb=" O PHE c 32 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 91 through 92 removed outlier: 8.400A pdb=" N VAL c 92 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE c 69 " --> pdb=" O VAL c 92 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU c 68 " --> pdb=" O TRP c 162 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL c 164 " --> pdb=" O LEU c 68 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL c 70 " --> pdb=" O VAL c 164 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL c 161 " --> pdb=" O ILE c 184 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ILE c 186 " --> pdb=" O VAL c 161 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL c 163 " --> pdb=" O ILE c 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'w' and resid 3 through 6 removed outlier: 5.499A pdb=" N HIS w 35 " --> pdb=" O ASP w 59 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASP w 59 " --> pdb=" O HIS w 35 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'w' and resid 143 through 144 Processing sheet with id=AD2, first strand: chain 'w' and resid 211 through 212 1070 hydrogen bonds defined for protein. 3081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1328 hydrogen bonds 2050 hydrogen bond angles 0 basepair planarities 521 basepair parallelities 769 stacking parallelities Total time for adding SS restraints: 39.51 Time building geometry restraints manager: 11.97 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: 7702 1.33 - 1.45: 23908 1.45 - 1.57: 23951 1.57 - 1.70: 3032 1.70 - 1.82: 84 Bond restraints: 58677 Sorted by residual: bond pdb=" CB PRO c 182 " pdb=" CG PRO c 182 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.11e+00 bond pdb=" C ARG w 131 " pdb=" O ARG w 131 " ideal model delta sigma weight residual 1.236 1.206 0.030 1.16e-02 7.43e+03 6.85e+00 bond pdb=" CB PRO d 108 " pdb=" CG PRO d 108 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.18e+00 bond pdb=" CB PRO h 58 " pdb=" CG PRO h 58 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.81e+00 bond pdb=" CG PRO d 108 " pdb=" CD PRO d 108 " ideal model delta sigma weight residual 1.503 1.566 -0.063 3.40e-02 8.65e+02 3.43e+00 ... (remaining 58672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 85983 2.38 - 4.76: 683 4.76 - 7.13: 74 7.13 - 9.51: 15 9.51 - 11.89: 6 Bond angle restraints: 86761 Sorted by residual: angle pdb=" CA PRO c 182 " pdb=" N PRO c 182 " pdb=" CD PRO c 182 " ideal model delta sigma weight residual 112.00 100.70 11.30 1.40e+00 5.10e-01 6.51e+01 angle pdb=" CA PRO h 58 " pdb=" N PRO h 58 " pdb=" CD PRO h 58 " ideal model delta sigma weight residual 112.00 100.73 11.27 1.40e+00 5.10e-01 6.48e+01 angle pdb=" CA PRO d 108 " pdb=" N PRO d 108 " pdb=" CD PRO d 108 " ideal model delta sigma weight residual 112.00 102.38 9.62 1.40e+00 5.10e-01 4.72e+01 angle pdb=" C SER u 48 " pdb=" N GLU u 49 " pdb=" CA GLU u 49 " ideal model delta sigma weight residual 121.14 113.09 8.05 1.75e+00 3.27e-01 2.12e+01 angle pdb=" C ARG k 23 " pdb=" N LYS k 24 " pdb=" CA LYS k 24 " ideal model delta sigma weight residual 121.14 113.46 7.68 1.75e+00 3.27e-01 1.92e+01 ... (remaining 86756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 33317 35.99 - 71.97: 3996 71.97 - 107.96: 433 107.96 - 143.94: 15 143.94 - 179.93: 17 Dihedral angle restraints: 37778 sinusoidal: 29825 harmonic: 7953 Sorted by residual: dihedral pdb=" O4' U a1303 " pdb=" C1' U a1303 " pdb=" N1 U a1303 " pdb=" C2 U a1303 " ideal model delta sinusoidal sigma weight residual 200.00 39.12 160.88 1 1.50e+01 4.44e-03 8.30e+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 0.51 -160.51 1 1.50e+01 4.44e-03 8.29e+01 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 42.82 157.18 1 1.50e+01 4.44e-03 8.20e+01 ... (remaining 37775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 9906 0.055 - 0.111: 866 0.111 - 0.166: 130 0.166 - 0.221: 22 0.221 - 0.277: 4 Chirality restraints: 10928 Sorted by residual: 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 2.19 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CG LEU n 56 " pdb=" CB LEU n 56 " pdb=" CD1 LEU n 56 " pdb=" CD2 LEU n 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 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 -2.51 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 10925 not shown) Planarity restraints: 5394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP h 57 " 0.100 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO h 58 " -0.247 5.00e-02 4.00e+02 pdb=" CA PRO h 58 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO h 58 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE c 181 " 0.065 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO c 182 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO c 182 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO c 182 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN d 107 " 0.061 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO d 108 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO d 108 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO d 108 " 0.048 5.00e-02 4.00e+02 ... (remaining 5391 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 439 2.54 - 3.13: 39723 3.13 - 3.72: 104680 3.72 - 4.31: 143969 4.31 - 4.90: 202900 Nonbonded interactions: 491711 Sorted by model distance: nonbonded pdb=" O2 U a 83 " pdb=" O6 G a 86 " model vdw 1.955 2.432 nonbonded pdb=" O2' A a 728 " pdb=" N7 A a 729 " model vdw 2.072 3.120 nonbonded pdb=" O2' U a 438 " pdb=" O2 U a 439 " model vdw 2.142 3.040 nonbonded pdb=" OP2 U a1265 " pdb=" O2' U a1266 " model vdw 2.171 3.040 nonbonded pdb=" N6 A a 149 " pdb=" O2 C a 166 " model vdw 2.187 3.120 ... (remaining 491706 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.780 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 121.590 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 : 0.003 0.133 58677 Z= 0.167 Angle : 0.560 11.890 86761 Z= 0.293 Chirality : 0.034 0.277 10928 Planarity : 0.005 0.143 5394 Dihedral : 23.546 179.929 32656 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.43 % Allowed : 31.17 % Favored : 68.39 % 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: 0.56 (0.16), residues: 2725 helix: 1.77 (0.16), residues: 1037 sheet: 0.14 (0.24), residues: 487 loop : -0.76 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP w 96 HIS 0.010 0.001 HIS t 83 PHE 0.042 0.001 PHE b 22 TYR 0.040 0.001 TYR c 49 ARG 0.014 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 133 MET cc_start: 0.8536 (mtm) cc_final: 0.8038 (mpp) REVERT: d 147 LYS cc_start: 0.8799 (tttp) cc_final: 0.8372 (tttt) REVERT: d 168 TYR cc_start: 0.8029 (m-80) cc_final: 0.7568 (m-80) REVERT: e 150 PHE cc_start: 0.8609 (m-80) cc_final: 0.8381 (m-80) outliers start: 10 outliers final: 8 residues processed: 213 average time/residue: 0.5772 time to fit residues: 202.0335 Evaluate side-chains 206 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 32 TYR Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 142 ARG Chi-restraints excluded: chain e residue 139 ASP Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain u residue 45 ASP Chi-restraints excluded: chain w residue 131 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 9.9990 chunk 318 optimal weight: 0.6980 chunk 176 optimal weight: 0.0970 chunk 108 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 chunk 329 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 245 optimal weight: 0.7980 chunk 381 optimal weight: 6.9990 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 51 GLN e 185 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 ASN j 66 GLN q 107 ASN ** w 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 58677 Z= 0.164 Angle : 0.535 8.834 86761 Z= 0.276 Chirality : 0.034 0.281 10928 Planarity : 0.004 0.084 5394 Dihedral : 23.610 179.494 27107 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.50 % Allowed : 28.20 % Favored : 69.30 % 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: 0.72 (0.17), residues: 2725 helix: 1.88 (0.16), residues: 1053 sheet: 0.23 (0.23), residues: 501 loop : -0.69 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP w 96 HIS 0.005 0.001 HIS w 30 PHE 0.012 0.001 PHE c 104 TYR 0.015 0.001 TYR w 175 ARG 0.019 0.000 ARG w 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 6 ASN cc_start: 0.8458 (t0) cc_final: 0.8190 (t0) REVERT: d 138 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8897 (pp30) REVERT: d 147 LYS cc_start: 0.8700 (tttp) cc_final: 0.8213 (tttt) REVERT: f 37 ILE cc_start: 0.8690 (pp) cc_final: 0.8485 (pt) REVERT: g 33 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7866 (t0) REVERT: g 41 ASP cc_start: 0.8354 (t70) cc_final: 0.7955 (p0) REVERT: h 22 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8986 (tp) REVERT: h 49 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8146 (tm-30) REVERT: i 48 ASP cc_start: 0.8081 (t0) cc_final: 0.7794 (t0) REVERT: i 63 GLN cc_start: 0.8496 (mp10) cc_final: 0.8102 (mp10) REVERT: k 45 GLU cc_start: 0.7350 (tp30) cc_final: 0.7098 (tp30) REVERT: k 66 GLU cc_start: 0.6456 (pm20) cc_final: 0.6147 (pm20) REVERT: l 45 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8214 (p0) REVERT: l 103 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7491 (mm-30) REVERT: q 112 GLU cc_start: 0.8369 (pp20) cc_final: 0.8104 (pp20) REVERT: u 45 ASP cc_start: 0.8321 (p0) cc_final: 0.7707 (p0) REVERT: u 49 GLU cc_start: 0.8088 (pm20) cc_final: 0.7842 (pm20) REVERT: c 49 TYR cc_start: 0.8354 (m-80) cc_final: 0.7929 (m-80) REVERT: w 57 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.7964 (m-40) outliers start: 58 outliers final: 23 residues processed: 269 average time/residue: 0.5472 time to fit residues: 247.4131 Evaluate side-chains 225 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 32 TYR Chi-restraints excluded: chain d residue 33 LYS Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 185 GLN Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain w residue 57 ASN Chi-restraints excluded: chain w residue 92 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 382 optimal weight: 5.9990 chunk 412 optimal weight: 30.0000 chunk 340 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 306 optimal weight: 0.8980 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 78 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 58677 Z= 0.352 Angle : 0.615 9.025 86761 Z= 0.318 Chirality : 0.038 0.294 10928 Planarity : 0.005 0.074 5394 Dihedral : 23.565 178.802 27093 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.80 % Allowed : 27.16 % Favored : 69.04 % 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: 0.60 (0.16), residues: 2725 helix: 1.78 (0.16), residues: 1057 sheet: 0.16 (0.24), residues: 496 loop : -0.75 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP w 96 HIS 0.005 0.001 HIS k 15 PHE 0.018 0.002 PHE c 104 TYR 0.015 0.002 TYR w 246 ARG 0.008 0.001 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 215 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 6 ASN cc_start: 0.8724 (t0) cc_final: 0.8481 (t0) REVERT: d 126 ARG cc_start: 0.7843 (mmt180) cc_final: 0.7360 (mmp80) REVERT: d 138 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9014 (mm-40) REVERT: e 80 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7760 (ptmt) REVERT: g 43 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.7114 (p-90) REVERT: h 22 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9308 (tp) REVERT: h 49 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8158 (tm-30) REVERT: i 48 ASP cc_start: 0.8291 (t0) cc_final: 0.7954 (t0) REVERT: i 63 GLN cc_start: 0.8383 (mp10) cc_final: 0.8055 (mp10) REVERT: k 45 GLU cc_start: 0.7358 (tp30) cc_final: 0.7125 (tp30) REVERT: k 66 GLU cc_start: 0.6433 (pm20) cc_final: 0.6146 (pm20) REVERT: l 103 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7496 (mm-30) REVERT: n 43 MET cc_start: 0.8054 (ppp) cc_final: 0.7789 (ppp) REVERT: o 61 TRP cc_start: 0.8534 (OUTLIER) cc_final: 0.7496 (p90) REVERT: q 112 GLU cc_start: 0.8392 (pp20) cc_final: 0.8042 (pp20) REVERT: t 25 LYS cc_start: 0.8365 (pmtt) cc_final: 0.8128 (pmtt) REVERT: c 49 TYR cc_start: 0.8673 (m-80) cc_final: 0.8432 (m-80) REVERT: x 62 GLU cc_start: 0.9307 (mm-30) cc_final: 0.9070 (mm-30) outliers start: 88 outliers final: 49 residues processed: 284 average time/residue: 0.5662 time to fit residues: 265.2673 Evaluate side-chains 249 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 32 TYR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 126 VAL Chi-restraints excluded: chain d residue 33 LYS Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 38 ARG Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain e residue 108 MET 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 186 ILE Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 67 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 16 PHE Chi-restraints excluded: chain o residue 61 TRP Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain r residue 94 LEU Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 108 HIS Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 254 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 383 optimal weight: 5.9990 chunk 405 optimal weight: 50.0000 chunk 200 optimal weight: 5.9990 chunk 363 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 111 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 58677 Z= 0.355 Angle : 0.612 9.252 86761 Z= 0.316 Chirality : 0.039 0.295 10928 Planarity : 0.005 0.066 5394 Dihedral : 23.545 178.298 27093 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.01 % Allowed : 27.03 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.16), residues: 2725 helix: 1.68 (0.16), residues: 1069 sheet: 0.11 (0.24), residues: 494 loop : -0.78 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.019 0.002 PHE c 104 TYR 0.018 0.002 TYR w 123 ARG 0.016 0.001 ARG w 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 217 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 6 ASN cc_start: 0.8665 (t0) cc_final: 0.8395 (t0) REVERT: d 126 ARG cc_start: 0.8022 (mmt180) cc_final: 0.7493 (mmp80) REVERT: d 138 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8983 (mm-40) REVERT: d 142 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8474 (mtm180) REVERT: d 147 LYS cc_start: 0.8808 (tttp) cc_final: 0.8571 (tttp) REVERT: e 80 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7781 (ptmt) REVERT: g 43 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.7075 (p-90) REVERT: h 22 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9329 (tp) REVERT: h 49 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8145 (tm-30) REVERT: i 48 ASP cc_start: 0.8401 (t0) cc_final: 0.8031 (t0) REVERT: i 63 GLN cc_start: 0.8357 (mp10) cc_final: 0.8041 (mp10) REVERT: k 45 GLU cc_start: 0.7378 (tp30) cc_final: 0.7046 (tp30) REVERT: l 103 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7340 (mm-30) REVERT: o 11 ASN cc_start: 0.9132 (m110) cc_final: 0.8907 (m-40) REVERT: o 61 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.7726 (p90) REVERT: q 112 GLU cc_start: 0.8379 (pp20) cc_final: 0.8028 (pp20) REVERT: t 25 LYS cc_start: 0.8458 (pmtt) cc_final: 0.8227 (pmtt) REVERT: w 34 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8765 (mt) REVERT: w 139 PHE cc_start: 0.5681 (OUTLIER) cc_final: 0.5362 (t80) outliers start: 116 outliers final: 69 residues processed: 311 average time/residue: 0.5731 time to fit residues: 294.7534 Evaluate side-chains 280 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 204 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 32 TYR Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain d residue 33 LYS Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 142 ARG Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 38 ARG Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 96 VAL 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 42 SER Chi-restraints excluded: chain f residue 97 PHE Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 67 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 16 PHE Chi-restraints excluded: chain o residue 61 TRP Chi-restraints excluded: chain p residue 9 LYS Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain q residue 3 VAL Chi-restraints excluded: chain q residue 13 ILE Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 5 LYS Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain r residue 94 LEU Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain c residue 108 HIS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 254 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 302 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 346 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 364 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 58677 Z= 0.388 Angle : 0.637 10.317 86761 Z= 0.329 Chirality : 0.040 0.294 10928 Planarity : 0.005 0.061 5394 Dihedral : 23.553 178.009 27093 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.09 % Allowed : 26.90 % Favored : 68.01 % 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: 0.44 (0.16), residues: 2725 helix: 1.66 (0.16), residues: 1069 sheet: 0.02 (0.23), residues: 492 loop : -0.86 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.018 0.002 PHE c 104 TYR 0.034 0.002 TYR c 49 ARG 0.011 0.001 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 221 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 6 ASN cc_start: 0.8667 (t0) cc_final: 0.8380 (t0) REVERT: d 126 ARG cc_start: 0.8137 (mmt180) cc_final: 0.7649 (mmp80) REVERT: d 138 GLN cc_start: 0.9293 (mm-40) cc_final: 0.9019 (mm-40) REVERT: e 80 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7800 (ptmt) REVERT: e 111 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8640 (tt0) REVERT: g 43 TRP cc_start: 0.8448 (OUTLIER) cc_final: 0.7035 (p-90) REVERT: h 22 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9381 (tp) REVERT: h 49 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8140 (tm-30) REVERT: i 48 ASP cc_start: 0.8485 (t0) cc_final: 0.8080 (t0) REVERT: i 63 GLN cc_start: 0.8307 (mp10) cc_final: 0.8047 (mp10) REVERT: k 45 GLU cc_start: 0.7349 (tp30) cc_final: 0.7037 (tp30) REVERT: k 66 GLU cc_start: 0.6720 (pm20) cc_final: 0.6426 (pm20) REVERT: l 103 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7202 (mm-30) REVERT: n 44 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6780 (mmt-90) REVERT: o 11 ASN cc_start: 0.9099 (m110) cc_final: 0.8810 (m-40) REVERT: o 61 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.7754 (p90) REVERT: p 88 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6035 (ptt180) REVERT: q 107 ASN cc_start: 0.9180 (m110) cc_final: 0.8913 (m110) REVERT: q 112 GLU cc_start: 0.8422 (pp20) cc_final: 0.8044 (pp20) REVERT: x 62 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9113 (mm-30) REVERT: w 34 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8721 (mt) REVERT: w 139 PHE cc_start: 0.5924 (OUTLIER) cc_final: 0.5608 (t80) outliers start: 118 outliers final: 80 residues processed: 318 average time/residue: 0.5646 time to fit residues: 298.1836 Evaluate side-chains 305 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 216 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 32 TYR Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain d residue 33 LYS Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 38 ARG Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 96 VAL 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 42 SER Chi-restraints excluded: chain f residue 97 PHE Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 67 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain l residue 137 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 44 ARG Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 78 ILE Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 16 PHE Chi-restraints excluded: chain o residue 24 CYS Chi-restraints excluded: chain o residue 61 TRP Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 88 ARG Chi-restraints excluded: chain q residue 3 VAL 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 5 LYS Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 108 HIS Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 146 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 254 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 10.0000 chunk 365 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 238 optimal weight: 1.9990 chunk 100 optimal weight: 30.0000 chunk 406 optimal weight: 10.0000 chunk 337 optimal weight: 4.9990 chunk 188 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 overall best weight: 5.7992 ------------------------------------------------------------------------------- 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** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 58677 Z= 0.327 Angle : 0.610 9.756 86761 Z= 0.316 Chirality : 0.038 0.283 10928 Planarity : 0.005 0.061 5394 Dihedral : 23.548 178.614 27093 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.75 % Allowed : 27.50 % Favored : 67.75 % 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: 0.47 (0.16), residues: 2725 helix: 1.69 (0.16), residues: 1070 sheet: 0.03 (0.23), residues: 489 loop : -0.85 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.017 0.002 PHE c 104 TYR 0.022 0.002 TYR c 49 ARG 0.012 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 218 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 6 ASN cc_start: 0.8654 (t0) cc_final: 0.8349 (t0) REVERT: d 126 ARG cc_start: 0.8092 (mmt180) cc_final: 0.7185 (mmp-170) REVERT: d 138 GLN cc_start: 0.9312 (mm-40) cc_final: 0.9038 (mm-40) REVERT: d 147 LYS cc_start: 0.8760 (tttp) cc_final: 0.8342 (tttm) REVERT: e 80 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7774 (ptmt) REVERT: e 111 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: g 43 TRP cc_start: 0.8528 (OUTLIER) cc_final: 0.7052 (p-90) REVERT: h 22 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9360 (tp) REVERT: h 49 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8148 (tm-30) REVERT: i 48 ASP cc_start: 0.8470 (t0) cc_final: 0.8046 (t0) REVERT: i 63 GLN cc_start: 0.8276 (mp10) cc_final: 0.7997 (mp10) REVERT: k 45 GLU cc_start: 0.7350 (tp30) cc_final: 0.7042 (tp30) REVERT: l 103 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6995 (mm-30) REVERT: n 44 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7639 (mmt-90) REVERT: o 11 ASN cc_start: 0.9085 (m110) cc_final: 0.8753 (m-40) REVERT: o 61 TRP cc_start: 0.8612 (OUTLIER) cc_final: 0.7715 (p90) REVERT: p 88 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6076 (ptt180) REVERT: q 107 ASN cc_start: 0.9173 (m110) cc_final: 0.8929 (m110) REVERT: q 112 GLU cc_start: 0.8448 (pp20) cc_final: 0.8056 (pp20) REVERT: t 17 LYS cc_start: 0.9353 (mtmt) cc_final: 0.8985 (pttt) REVERT: c 154 MET cc_start: 0.8595 (mtp) cc_final: 0.8387 (mmm) REVERT: x 62 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9067 (mm-30) REVERT: w 34 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8723 (mt) REVERT: w 139 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5663 (t80) REVERT: w 166 LYS cc_start: 0.9151 (ttmm) cc_final: 0.8790 (mtmm) REVERT: w 214 GLN cc_start: 0.9007 (pp30) cc_final: 0.8778 (mt0) outliers start: 110 outliers final: 82 residues processed: 308 average time/residue: 0.5694 time to fit residues: 287.8280 Evaluate side-chains 304 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 213 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 169 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain d residue 33 LYS Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 38 ARG Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 96 VAL 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 160 ARG Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 97 PHE Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain f residue 196 LYS Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 67 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 137 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 44 ARG Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 78 ILE Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 16 PHE Chi-restraints excluded: chain o residue 24 CYS Chi-restraints excluded: chain o residue 61 TRP Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 88 ARG Chi-restraints excluded: chain q residue 3 VAL 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 5 LYS Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 108 HIS Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 131 ARG Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 146 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 254 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 296 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 342 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 404 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 246 optimal weight: 0.0870 chunk 186 optimal weight: 20.0000 overall best weight: 4.6166 ------------------------------------------------------------------------------- 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** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 58677 Z= 0.269 Angle : 0.584 9.759 86761 Z= 0.302 Chirality : 0.037 0.274 10928 Planarity : 0.004 0.060 5394 Dihedral : 23.520 178.790 27091 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.32 % Allowed : 28.11 % Favored : 67.57 % 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: 0.58 (0.16), residues: 2725 helix: 1.81 (0.16), residues: 1063 sheet: 0.04 (0.23), residues: 490 loop : -0.78 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.014 0.001 PHE c 104 TYR 0.031 0.001 TYR c 49 ARG 0.011 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 220 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 6 ASN cc_start: 0.8661 (t0) cc_final: 0.8332 (t0) REVERT: d 126 ARG cc_start: 0.8024 (mmt180) cc_final: 0.7178 (mmp-170) REVERT: d 138 GLN cc_start: 0.9317 (mm-40) cc_final: 0.9072 (mm-40) REVERT: e 80 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7724 (ptmt) REVERT: e 111 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: e 135 TYR cc_start: 0.9204 (m-80) cc_final: 0.8611 (m-80) REVERT: g 43 TRP cc_start: 0.8555 (OUTLIER) cc_final: 0.7130 (p-90) REVERT: h 22 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9321 (tp) REVERT: h 49 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8146 (tm-30) REVERT: i 48 ASP cc_start: 0.8420 (t0) cc_final: 0.7987 (t0) REVERT: i 63 GLN cc_start: 0.8311 (mp10) cc_final: 0.8093 (mp10) REVERT: k 45 GLU cc_start: 0.7360 (tp30) cc_final: 0.7046 (tp30) REVERT: k 66 GLU cc_start: 0.6721 (pm20) cc_final: 0.6512 (pm20) REVERT: l 103 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6861 (mm-30) REVERT: l 128 ASN cc_start: 0.8211 (t0) cc_final: 0.7852 (t0) REVERT: n 44 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7680 (mmt-90) REVERT: o 11 ASN cc_start: 0.9063 (m110) cc_final: 0.8810 (m-40) REVERT: o 61 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.7697 (p90) REVERT: p 88 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5865 (ptt180) REVERT: q 107 ASN cc_start: 0.9190 (m110) cc_final: 0.8946 (m110) REVERT: q 112 GLU cc_start: 0.8462 (pp20) cc_final: 0.8045 (pp20) REVERT: t 17 LYS cc_start: 0.9360 (mtmt) cc_final: 0.8976 (pttt) REVERT: x 62 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9036 (mm-30) REVERT: w 34 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8696 (mt) REVERT: w 139 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.5472 (t80) outliers start: 100 outliers final: 78 residues processed: 304 average time/residue: 0.5707 time to fit residues: 286.0124 Evaluate side-chains 299 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 212 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 57 TYR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 169 ILE Chi-restraints excluded: chain b residue 185 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 38 ARG Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 96 VAL 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 42 SER Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain f residue 196 LYS Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 135 VAL Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 67 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 137 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 44 ARG Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 16 PHE Chi-restraints excluded: chain o residue 24 CYS Chi-restraints excluded: chain o residue 61 TRP Chi-restraints excluded: chain p residue 9 LYS Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 88 ARG Chi-restraints excluded: chain q residue 3 VAL 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 5 LYS Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 108 HIS Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 131 ARG Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 146 VAL Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 254 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 58677 Z= 0.389 Angle : 0.644 9.711 86761 Z= 0.332 Chirality : 0.040 0.291 10928 Planarity : 0.005 0.061 5394 Dihedral : 23.532 178.468 27091 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.88 % Allowed : 27.76 % Favored : 67.36 % 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: 0.40 (0.16), residues: 2725 helix: 1.64 (0.16), residues: 1074 sheet: -0.05 (0.23), residues: 491 loop : -0.90 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP w 96 HIS 0.007 0.001 HIS k 15 PHE 0.018 0.002 PHE f 97 TYR 0.025 0.002 TYR c 49 ARG 0.013 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 214 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 6 ASN cc_start: 0.8652 (t0) cc_final: 0.8327 (t0) REVERT: d 126 ARG cc_start: 0.8095 (mmt180) cc_final: 0.7212 (mmp-170) REVERT: d 138 GLN cc_start: 0.9306 (mm-40) cc_final: 0.9043 (mm-40) REVERT: d 147 LYS cc_start: 0.8765 (tttp) cc_final: 0.7937 (ttpp) REVERT: d 204 LYS cc_start: 0.8369 (ptpp) cc_final: 0.8108 (mttp) REVERT: e 80 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7874 (ptmt) REVERT: e 111 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: g 43 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.7096 (p-90) REVERT: h 49 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8157 (tm-30) REVERT: i 48 ASP cc_start: 0.8446 (t0) cc_final: 0.8009 (t0) REVERT: i 63 GLN cc_start: 0.8296 (mp10) cc_final: 0.8089 (mp10) REVERT: k 45 GLU cc_start: 0.7381 (tp30) cc_final: 0.7073 (tp30) REVERT: l 103 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6851 (mm-30) REVERT: n 44 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7684 (mmt-90) REVERT: o 11 ASN cc_start: 0.9083 (m110) cc_final: 0.8867 (m-40) REVERT: o 61 TRP cc_start: 0.8683 (OUTLIER) cc_final: 0.7864 (p90) REVERT: p 88 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.5816 (ptt180) REVERT: q 107 ASN cc_start: 0.9168 (m110) cc_final: 0.8924 (m110) REVERT: q 112 GLU cc_start: 0.8464 (pp20) cc_final: 0.8054 (pp20) REVERT: t 17 LYS cc_start: 0.9343 (mtmt) cc_final: 0.8977 (pttt) REVERT: c 49 TYR cc_start: 0.8851 (m-80) cc_final: 0.8640 (m-80) REVERT: c 154 MET cc_start: 0.8764 (mtp) cc_final: 0.8557 (mmm) REVERT: x 60 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7218 (mmm160) REVERT: x 62 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8995 (mm-30) REVERT: w 34 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8697 (mt) REVERT: w 139 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5771 (t80) REVERT: w 214 GLN cc_start: 0.9106 (pp30) cc_final: 0.8735 (mt0) outliers start: 113 outliers final: 91 residues processed: 312 average time/residue: 0.5807 time to fit residues: 298.0408 Evaluate side-chains 305 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 206 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 57 TYR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 169 ILE Chi-restraints excluded: chain b residue 185 LEU Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 207 ILE Chi-restraints excluded: chain e residue 38 ARG Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 96 VAL 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 160 ARG Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 97 PHE Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain f residue 196 LYS Chi-restraints excluded: chain g residue 8 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 43 TRP Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 135 VAL Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 67 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain l residue 137 ARG Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 44 ARG Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 78 ILE Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 16 PHE Chi-restraints excluded: chain o residue 24 CYS Chi-restraints excluded: chain o residue 61 TRP Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 88 ARG Chi-restraints excluded: chain q residue 3 VAL 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 5 LYS Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain s residue 53 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 108 HIS Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 66 ARG Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 131 ARG Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 146 VAL Chi-restraints excluded: chain w residue 173 VAL Chi-restraints excluded: chain w residue 205 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 8.9990 chunk 387 optimal weight: 3.9990 chunk 353 optimal weight: 2.9990 chunk 377 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 296 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 340 optimal weight: 0.9990 chunk 356 optimal weight: 1.9990 chunk 375 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 99 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 66 GLN ** c 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 58677 Z= 0.175 Angle : 0.563 9.757 86761 Z= 0.291 Chirality : 0.035 0.261 10928 Planarity : 0.004 0.063 5394 Dihedral : 23.508 179.567 27091 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.20 % Allowed : 29.32 % Favored : 67.49 % 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: 0.65 (0.16), residues: 2725 helix: 1.87 (0.16), residues: 1062 sheet: 0.10 (0.23), residues: 489 loop : -0.75 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.012 0.001 PHE c 104 TYR 0.022 0.001 TYR c 49 ARG 0.014 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 217 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 6 ASN cc_start: 0.8597 (t0) cc_final: 0.8253 (t0) REVERT: d 126 ARG cc_start: 0.8034 (mmt180) cc_final: 0.7162 (mmp-170) REVERT: d 138 GLN cc_start: 0.9336 (mm-40) cc_final: 0.9069 (mm-40) REVERT: d 147 LYS cc_start: 0.8758 (tttp) cc_final: 0.8501 (tttp) REVERT: d 168 TYR cc_start: 0.8047 (m-80) cc_final: 0.7494 (m-80) REVERT: e 80 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7586 (ptmt) REVERT: e 135 TYR cc_start: 0.9174 (m-80) cc_final: 0.8611 (m-80) REVERT: h 49 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8136 (tm-30) REVERT: i 48 ASP cc_start: 0.8400 (t0) cc_final: 0.8021 (t0) REVERT: k 45 GLU cc_start: 0.7461 (tp30) cc_final: 0.7138 (tp30) REVERT: l 103 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6799 (mm-30) REVERT: l 128 ASN cc_start: 0.8072 (t0) cc_final: 0.7748 (t0) REVERT: n 44 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7656 (mmt-90) REVERT: o 11 ASN cc_start: 0.9061 (m110) cc_final: 0.8860 (m-40) REVERT: o 61 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.7620 (p90) REVERT: p 88 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5737 (ptt180) REVERT: q 107 ASN cc_start: 0.9197 (m110) cc_final: 0.8959 (m110) REVERT: q 112 GLU cc_start: 0.8443 (pp20) cc_final: 0.8009 (pp20) REVERT: t 17 LYS cc_start: 0.9348 (mtmt) cc_final: 0.8966 (pttt) REVERT: c 49 TYR cc_start: 0.8766 (m-80) cc_final: 0.8517 (m-80) REVERT: c 154 MET cc_start: 0.8712 (mtp) cc_final: 0.8507 (mmm) REVERT: x 60 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7234 (mmm160) REVERT: x 62 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8978 (mm-30) REVERT: w 34 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8688 (mt) REVERT: w 139 PHE cc_start: 0.5981 (OUTLIER) cc_final: 0.5579 (t80) REVERT: w 214 GLN cc_start: 0.9069 (pp30) cc_final: 0.8680 (mt0) outliers start: 74 outliers final: 58 residues processed: 278 average time/residue: 0.5734 time to fit residues: 263.8917 Evaluate side-chains 269 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 117 GLU Chi-restraints excluded: chain b residue 185 LEU Chi-restraints excluded: chain v residue 31 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 82 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 142 ARG Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 38 ARG Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 135 VAL Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 67 MET Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 44 ARG Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 78 ILE Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 16 PHE Chi-restraints excluded: chain o residue 24 CYS Chi-restraints excluded: chain o residue 61 TRP Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 88 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 92 GLU Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 108 HIS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 131 ARG Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 146 VAL Chi-restraints excluded: chain w residue 205 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 0.9990 chunk 398 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 418 optimal weight: 6.9990 chunk 385 optimal weight: 20.0000 chunk 333 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 204 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 66 GLN l 47 GLN l 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 58677 Z= 0.182 Angle : 0.555 9.766 86761 Z= 0.286 Chirality : 0.034 0.251 10928 Planarity : 0.004 0.061 5394 Dihedral : 23.465 179.025 27091 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.15 % Allowed : 29.84 % Favored : 67.01 % 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: 0.73 (0.16), residues: 2725 helix: 1.90 (0.16), residues: 1061 sheet: 0.19 (0.23), residues: 489 loop : -0.69 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.011 0.001 PHE c 104 TYR 0.022 0.001 TYR d 187 ARG 0.014 0.000 ARG l 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5450 Ramachandran restraints generated. 2725 Oldfield, 0 Emsley, 2725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 6 ASN cc_start: 0.8616 (t0) cc_final: 0.8322 (t0) REVERT: d 126 ARG cc_start: 0.8071 (mmt180) cc_final: 0.7207 (mmp-170) REVERT: d 138 GLN cc_start: 0.9331 (mm-40) cc_final: 0.9063 (mm-40) REVERT: d 147 LYS cc_start: 0.8747 (tttp) cc_final: 0.8446 (tttp) REVERT: d 204 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8062 (mttp) REVERT: e 80 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7459 (ptmt) REVERT: e 135 TYR cc_start: 0.9175 (m-80) cc_final: 0.8613 (m-80) REVERT: h 49 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8110 (tm-30) REVERT: i 48 ASP cc_start: 0.8357 (t0) cc_final: 0.8112 (t0) REVERT: k 45 GLU cc_start: 0.7479 (tp30) cc_final: 0.7169 (tp30) REVERT: l 103 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6842 (mm-30) REVERT: l 128 ASN cc_start: 0.8058 (t0) cc_final: 0.7713 (t0) REVERT: o 11 ASN cc_start: 0.9057 (m110) cc_final: 0.8856 (m-40) REVERT: o 61 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.7598 (p90) REVERT: q 107 ASN cc_start: 0.9181 (m110) cc_final: 0.8949 (m110) REVERT: q 112 GLU cc_start: 0.8445 (pp20) cc_final: 0.8033 (pp20) REVERT: t 17 LYS cc_start: 0.9356 (mtmt) cc_final: 0.8978 (pttt) REVERT: c 49 TYR cc_start: 0.8768 (m-80) cc_final: 0.8509 (m-80) REVERT: c 154 MET cc_start: 0.8720 (mtp) cc_final: 0.8418 (mmm) REVERT: x 60 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7183 (mmm160) REVERT: x 62 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8918 (mm-30) REVERT: w 34 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8677 (mt) REVERT: w 139 PHE cc_start: 0.5997 (OUTLIER) cc_final: 0.5613 (t80) REVERT: w 214 GLN cc_start: 0.9035 (pp30) cc_final: 0.8519 (mt0) outliers start: 73 outliers final: 60 residues processed: 270 average time/residue: 0.5539 time to fit residues: 248.5936 Evaluate side-chains 272 residues out of total 2317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 208 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 185 LEU Chi-restraints excluded: chain v residue 31 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 125 ASN Chi-restraints excluded: chain d residue 142 ARG Chi-restraints excluded: chain d residue 191 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 38 ARG Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 186 ILE Chi-restraints excluded: chain g residue 18 THR Chi-restraints excluded: chain g residue 29 VAL Chi-restraints excluded: chain g residue 76 ASP Chi-restraints excluded: chain h residue 135 VAL Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 76 ILE Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 47 GLN Chi-restraints excluded: chain l residue 91 VAL Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 5 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 78 ILE Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 16 PHE Chi-restraints excluded: chain o residue 24 CYS Chi-restraints excluded: chain o residue 61 TRP Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain q residue 3 VAL 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 92 GLU Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 51 VAL Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 3 VAL Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 108 HIS Chi-restraints excluded: chain c residue 157 VAL Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain w residue 92 ILE Chi-restraints excluded: chain w residue 131 ARG Chi-restraints excluded: chain w residue 139 PHE Chi-restraints excluded: chain w residue 146 VAL Chi-restraints excluded: chain w residue 205 SER Chi-restraints excluded: chain w residue 254 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 333 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.035618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.027773 restraints weight = 471146.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.028033 restraints weight = 196803.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.028352 restraints weight = 129941.053| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.304 58677 Z= 0.364 Angle : 0.622 59.200 86761 Z= 0.331 Chirality : 0.039 0.778 10928 Planarity : 0.004 0.059 5394 Dihedral : 23.458 179.102 27089 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.07 % Allowed : 29.97 % Favored : 66.97 % Cbeta Deviations : 0.04 % 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: 0.72 (0.16), residues: 2725 helix: 1.87 (0.16), residues: 1061 sheet: 0.20 (0.23), residues: 489 loop : -0.69 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP w 96 HIS 0.006 0.001 HIS k 15 PHE 0.012 0.001 PHE f 97 TYR 0.034 0.002 TYR d 168 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: 6556.50 seconds wall clock time: 119 minutes 22.90 seconds (7162.90 seconds total)