Starting phenix.real_space_refine on Wed Feb 21 14:37:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/02_2024/5v7q_8641_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/02_2024/5v7q_8641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/02_2024/5v7q_8641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/02_2024/5v7q_8641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/02_2024/5v7q_8641_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7q_8641/02_2024/5v7q_8641_updated.pdb" } resolution = 3.7 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= 0.002 sd= 0.012 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 3233 5.49 5 S 53 5.16 5 C 46406 2.51 5 N 17745 2.21 5 O 26869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q ASP 97": "OD1" <-> "OD2" Residue "R TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 94306 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 421 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 358 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 345 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "A" Number of atoms: 66956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3118, 66956 Classifications: {'RNA': 3118} Modifications used: {'rna2p_pur': 299, 'rna2p_pyr': 163, 'rna3p_pur': 1484, 'rna3p_pyr': 1172} Link IDs: {'rna2p': 462, 'rna3p': 2655} Chain breaks: 1 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 11, 'rna3p': 103} Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 9, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1335 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1060 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 886 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 742 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 759 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "X" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 476 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Y" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 541 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'917': 1} Classifications: {'undetermined': 1} Time building chain proxies: 36.94, per 1000 atoms: 0.39 Number of scatterers: 94306 At special positions: 0 Unit cell: (213.815, 225.295, 233.905, 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 53 16.00 P 3233 15.00 O 26869 8.00 N 17745 7.00 C 46406 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 - 3.50 Amino acid : False - 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: 42.14 Conformation dependent library (CDL) restraints added in 4.2 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 42 sheets defined 22.7% alpha, 14.7% beta 795 base pairs and 1585 stacking pairs defined. Time for finding SS restraints: 44.69 Creating SS restraints... Processing helix chain '0' and resid 10 through 18 removed outlier: 4.218A pdb=" N SER 0 15 " --> pdb=" O SER 0 11 " (cutoff:3.500A) Processing helix chain '0' and resid 41 through 49 removed outlier: 4.866A pdb=" N LYS 0 45 " --> pdb=" O ARG 0 42 " (cutoff:3.500A) Processing helix chain '2' and resid 12 through 19 Processing helix chain '2' and resid 21 through 26 removed outlier: 3.838A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 40 removed outlier: 3.551A pdb=" N SER 2 32 " --> pdb=" O ARG 2 28 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 11 No H-bonds generated for 'chain '3' and resid 8 through 11' Processing helix chain '3' and resid 38 through 44 Processing helix chain '3' and resid 55 through 62 removed outlier: 4.343A pdb=" N SER 3 60 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) Processing helix chain '6' and resid 39 through 41 No H-bonds generated for 'chain '6' and resid 39 through 41' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'D' and resid 42 through 45 No H-bonds generated for 'chain 'D' and resid 42 through 45' Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 126 through 129 No H-bonds generated for 'chain 'D' and resid 126 through 129' Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 37 through 51 Processing helix chain 'E' and resid 110 through 126 Processing helix chain 'E' and resid 144 through 154 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 192 through 196 Processing helix chain 'E' and resid 204 through 213 Processing helix chain 'F' and resid 13 through 26 Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 55 through 67 removed outlier: 4.312A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 108 Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'G' and resid 4 through 6 No H-bonds generated for 'chain 'G' and resid 4 through 6' Processing helix chain 'G' and resid 61 through 81 Processing helix chain 'G' and resid 139 through 148 removed outlier: 3.623A pdb=" N ILE G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 46 Processing helix chain 'J' and resid 25 through 37 Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 66 through 69 No H-bonds generated for 'chain 'J' and resid 66 through 69' Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 97 through 108 Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.728A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 117 No H-bonds generated for 'chain 'K' and resid 114 through 117' Processing helix chain 'L' and resid 5 through 7 No H-bonds generated for 'chain 'L' and resid 5 through 7' Processing helix chain 'L' and resid 39 through 42 No H-bonds generated for 'chain 'L' and resid 39 through 42' Processing helix chain 'L' and resid 56 through 59 No H-bonds generated for 'chain 'L' and resid 56 through 59' Processing helix chain 'L' and resid 79 through 85 Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'M' and resid 44 through 57 Processing helix chain 'M' and resid 111 through 124 Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 57 Proline residue: N 46 - end of helix removed outlier: 3.619A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 67 Processing helix chain 'N' and resid 74 through 81 Processing helix chain 'N' and resid 83 through 89 removed outlier: 4.868A pdb=" N ASP N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 22 removed outlier: 3.671A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 72 through 90 removed outlier: 3.964A pdb=" N VAL O 77 " --> pdb=" O LYS O 73 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 117 Processing helix chain 'P' and resid 2 through 11 Proline residue: P 10 - end of helix Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'Q' and resid 7 through 21 removed outlier: 3.883A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 71 removed outlier: 3.857A pdb=" N GLU Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 86 Processing helix chain 'Q' and resid 92 through 101 removed outlier: 3.687A pdb=" N ILE Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'S' and resid 24 through 34 removed outlier: 4.101A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 47 Processing helix chain 'S' and resid 55 through 70 Processing helix chain 'S' and resid 99 through 101 No H-bonds generated for 'chain 'S' and resid 99 through 101' Processing helix chain 'T' and resid 18 through 22 Processing helix chain 'T' and resid 25 through 27 No H-bonds generated for 'chain 'T' and resid 25 through 27' Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 68 through 70 No H-bonds generated for 'chain 'U' and resid 68 through 70' Processing helix chain 'V' and resid 19 through 27 Processing helix chain 'V' and resid 53 through 56 No H-bonds generated for 'chain 'V' and resid 53 through 56' Processing helix chain 'X' and resid 53 through 57 Processing helix chain 'Y' and resid 7 through 11 Processing helix chain 'Y' and resid 16 through 38 Processing helix chain 'Y' and resid 46 through 65 Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 43 through 49 Processing sheet with id= A, first strand: chain '1' and resid 37 through 42 Processing sheet with id= B, first strand: chain '1' and resid 11 through 14 removed outlier: 3.687A pdb=" N TYR 1 23 " --> pdb=" O LEU 1 13 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '3' and resid 14 through 16 removed outlier: 3.727A pdb=" N ARG 3 15 " --> pdb=" O VAL 3 23 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL 3 23 " --> pdb=" O ARG 3 15 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '4' and resid 15 through 19 Processing sheet with id= E, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= F, first strand: chain 'C' and resid 101 through 106 removed outlier: 3.864A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS C 96 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL C 79 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= H, first strand: chain 'C' and resid 172 through 176 Processing sheet with id= I, first strand: chain 'D' and resid 5 through 9 removed outlier: 6.085A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 13 through 17 removed outlier: 5.808A pdb=" N LYS D 195 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL D 182 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= L, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.500A pdb=" N GLY D 122 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 170 " --> pdb=" O GLY D 122 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 130 through 132 removed outlier: 6.632A pdb=" N VAL E 200 " --> pdb=" O HIS E 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 160 through 163 Processing sheet with id= O, first strand: chain 'F' and resid 94 through 98 removed outlier: 7.326A pdb=" N VAL F 164 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL F 41 " --> pdb=" O ASN F 162 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN F 162 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL F 43 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP F 160 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 23 through 26 Processing sheet with id= Q, first strand: chain 'G' and resid 42 through 45 Processing sheet with id= R, first strand: chain 'G' and resid 84 through 89 removed outlier: 6.330A pdb=" N THR G 133 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL G 126 " --> pdb=" O THR G 133 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER G 135 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE G 124 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 3 through 5 Processing sheet with id= T, first strand: chain 'J' and resid 137 through 139 removed outlier: 6.803A pdb=" N TRP J 15 " --> pdb=" O VAL J 138 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE J 18 " --> pdb=" O PHE J 53 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE J 55 " --> pdb=" O ILE J 18 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= V, first strand: chain 'K' and resid 7 through 9 removed outlier: 6.742A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 75 through 78 Processing sheet with id= X, first strand: chain 'M' and resid 40 through 43 removed outlier: 3.994A pdb=" N TRP M 92 " --> pdb=" O LEU M 74 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.583A pdb=" N MET N 110 " --> pdb=" O ILE N 100 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 32 through 37 removed outlier: 4.437A pdb=" N ALA O 56 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 82 through 87 removed outlier: 3.965A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR P 24 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N LYS P 43 " --> pdb=" O GLU P 63 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU P 63 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG P 49 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR P 57 " --> pdb=" O ARG P 49 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'R' and resid 13 through 17 removed outlier: 3.627A pdb=" N LEU R 42 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS R 9 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL R 40 " --> pdb=" O LYS R 9 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 21 through 26 removed outlier: 3.957A pdb=" N GLY R 63 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 74 through 79 Processing sheet with id= AE, first strand: chain 'S' and resid 13 through 17 removed outlier: 3.734A pdb=" N THR S 83 " --> pdb=" O VAL S 116 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU S 118 " --> pdb=" O VAL S 81 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL S 81 " --> pdb=" O GLU S 118 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'S' and resid 92 through 97 removed outlier: 3.683A pdb=" N ALA S 92 " --> pdb=" O ARG S 108 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.679A pdb=" N LEU T 32 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR T 30 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER T 56 " --> pdb=" O THR T 85 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'U' and resid 20 through 22 Processing sheet with id= AI, first strand: chain 'U' and resid 65 through 67 removed outlier: 3.794A pdb=" N GLN U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 7 through 10 Processing sheet with id= AK, first strand: chain 'V' and resid 41 through 45 removed outlier: 3.725A pdb=" N ILE V 31 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS V 82 " --> pdb=" O GLN V 91 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'V' and resid 105 through 109 Processing sheet with id= AM, first strand: chain 'V' and resid 121 through 124 Processing sheet with id= AN, first strand: chain 'X' and resid 13 through 16 Processing sheet with id= AO, first strand: chain 'X' and resid 33 through 36 Processing sheet with id= AP, first strand: chain 'Z' and resid 35 through 37 670 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2062 hydrogen bonds 3530 hydrogen bond angles 0 basepair planarities 795 basepair parallelities 1585 stacking parallelities Total time for adding SS restraints: 144.29 Time building geometry restraints manager: 45.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8727 1.31 - 1.43: 46959 1.43 - 1.56: 40745 1.56 - 1.69: 6464 1.69 - 1.81: 88 Bond restraints: 102983 Sorted by residual: bond pdb=" C02 917 A5001 " pdb=" N04 917 A5001 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C09 917 A5001 " pdb=" O11 917 A5001 " ideal model delta sigma weight residual 1.336 1.439 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C09 917 A5001 " pdb=" N08 917 A5001 " ideal model delta sigma weight residual 1.366 1.453 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C15 917 A5001 " pdb=" C18 917 A5001 " ideal model delta sigma weight residual 1.459 1.385 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CB PHE 2 21 " pdb=" CG PHE 2 21 " ideal model delta sigma weight residual 1.502 1.439 0.063 2.30e-02 1.89e+03 7.45e+00 ... (remaining 102978 not shown) Histogram of bond angle deviations from ideal: 94.99 - 103.18: 7839 103.18 - 111.38: 56973 111.38 - 119.57: 45083 119.57 - 127.76: 39040 127.76 - 135.96: 6297 Bond angle restraints: 155232 Sorted by residual: angle pdb=" N LYS K 113 " pdb=" CA LYS K 113 " pdb=" C LYS K 113 " ideal model delta sigma weight residual 114.62 109.18 5.44 1.14e+00 7.69e-01 2.28e+01 angle pdb=" O4' A A1272 " pdb=" C1' A A1272 " pdb=" N9 A A1272 " ideal model delta sigma weight residual 108.20 114.68 -6.48 1.50e+00 4.44e-01 1.87e+01 angle pdb=" N ARG N 9 " pdb=" CA ARG N 9 " pdb=" C ARG N 9 " ideal model delta sigma weight residual 110.53 105.01 5.52 1.29e+00 6.01e-01 1.83e+01 angle pdb=" O4' U A 719 " pdb=" C1' U A 719 " pdb=" N1 U A 719 " ideal model delta sigma weight residual 108.20 114.33 -6.13 1.50e+00 4.44e-01 1.67e+01 angle pdb=" C PHE R 79 " pdb=" N LYS R 80 " pdb=" CA LYS R 80 " ideal model delta sigma weight residual 121.71 116.30 5.41 1.39e+00 5.18e-01 1.52e+01 ... (remaining 155227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 58644 35.96 - 71.92: 6917 71.92 - 107.88: 745 107.88 - 143.85: 5 143.85 - 179.81: 12 Dihedral angle restraints: 66323 sinusoidal: 57265 harmonic: 9058 Sorted by residual: dihedral pdb=" O4' C A2309 " pdb=" C1' C A2309 " pdb=" N1 C A2309 " pdb=" C2 C A2309 " ideal model delta sinusoidal sigma weight residual -160.00 11.07 -171.07 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C A 946 " pdb=" C1' C A 946 " pdb=" N1 C A 946 " pdb=" C2 C A 946 " ideal model delta sinusoidal sigma weight residual -160.00 10.10 -170.10 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C A1517 " pdb=" C1' C A1517 " pdb=" N1 C A1517 " pdb=" C2 C A1517 " ideal model delta sinusoidal sigma weight residual 200.00 31.67 168.33 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 66320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 17876 0.071 - 0.143: 1910 0.143 - 0.214: 164 0.214 - 0.285: 15 0.285 - 0.357: 4 Chirality restraints: 19969 Sorted by residual: chirality pdb=" C1' U A2386 " pdb=" O4' U A2386 " pdb=" C2' U A2386 " pdb=" N1 U A2386 " both_signs ideal model delta sigma weight residual False 2.47 2.11 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C1' G A 880 " pdb=" O4' G A 880 " pdb=" C2' G A 880 " pdb=" N9 G A 880 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C3' U A1567 " pdb=" C4' U A1567 " pdb=" O3' U A1567 " pdb=" C2' U A1567 " both_signs ideal model delta sigma weight residual False -2.48 -2.18 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 19966 not shown) Planarity restraints: 7675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 107 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO C 108 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 108 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 108 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 69 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO M 70 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO M 70 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO M 70 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 31 " -0.060 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO H 32 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " -0.050 5.00e-02 4.00e+02 ... (remaining 7672 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 1779 2.60 - 3.17: 75777 3.17 - 3.75: 182051 3.75 - 4.32: 243328 4.32 - 4.90: 331939 Nonbonded interactions: 834874 Sorted by model distance: nonbonded pdb=" O2' G A2746 " pdb=" O2' U A2792 " model vdw 2.022 2.440 nonbonded pdb=" O2' G A 874 " pdb=" O2' G A 877 " model vdw 2.027 2.440 nonbonded pdb=" OG SER O 38 " pdb=" O HIS O 41 " model vdw 2.031 2.440 nonbonded pdb=" O2' U A1334 " pdb=" OH TYR E 192 " model vdw 2.046 2.440 nonbonded pdb=" OG1 THR F 136 " pdb=" OD1 ASN F 162 " model vdw 2.070 2.440 ... (remaining 834869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 6.290 Check model and map are aligned: 1.050 Set scattering table: 0.660 Process input model: 325.130 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 337.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 : 0.007 0.122 102983 Z= 0.405 Angle : 0.904 9.891 155232 Z= 0.468 Chirality : 0.046 0.357 19969 Planarity : 0.008 0.103 7675 Dihedral : 22.213 179.807 60517 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.60 % Allowed : 10.20 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -2.24 (0.14), residues: 3156 helix: -0.67 (0.17), residues: 770 sheet: -1.38 (0.21), residues: 552 loop : -1.93 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 104 HIS 0.026 0.004 HIS C 53 PHE 0.031 0.003 PHE Y 30 TYR 0.024 0.003 TYR J 80 ARG 0.020 0.002 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 883 time to evaluate : 3.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 8 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7936 (ttmm) REVERT: 1 31 ASN cc_start: 0.5928 (p0) cc_final: 0.5426 (p0) REVERT: 1 40 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8327 (mtpt) REVERT: 1 53 GLU cc_start: 0.7681 (mp0) cc_final: 0.7134 (mp0) REVERT: 4 24 MET cc_start: 0.7459 (ptp) cc_final: 0.7180 (ptp) REVERT: C 25 THR cc_start: 0.7768 (m) cc_final: 0.7551 (t) REVERT: C 78 LYS cc_start: 0.8220 (tttt) cc_final: 0.7660 (tptm) REVERT: C 84 TYR cc_start: 0.7895 (t80) cc_final: 0.7669 (t80) REVERT: C 155 LEU cc_start: 0.8639 (tp) cc_final: 0.7201 (tp) REVERT: C 169 GLU cc_start: 0.6376 (mt-10) cc_final: 0.6150 (mt-10) REVERT: C 192 THR cc_start: 0.8305 (m) cc_final: 0.7845 (p) REVERT: C 212 MET cc_start: 0.6983 (mmm) cc_final: 0.6763 (mmm) REVERT: D 48 SER cc_start: 0.7420 (t) cc_final: 0.7203 (p) REVERT: D 76 ASN cc_start: 0.7556 (t160) cc_final: 0.7337 (t0) REVERT: D 81 LEU cc_start: 0.8582 (tp) cc_final: 0.8205 (tp) REVERT: D 206 VAL cc_start: 0.8905 (t) cc_final: 0.8591 (p) REVERT: G 4 ILE cc_start: 0.8109 (tp) cc_final: 0.7760 (mt) REVERT: J 58 ASN cc_start: 0.6276 (t0) cc_final: 0.5934 (t0) REVERT: K 68 GLU cc_start: 0.6724 (mp0) cc_final: 0.6500 (mp0) REVERT: N 106 ASP cc_start: 0.7900 (p0) cc_final: 0.7567 (p0) REVERT: P 28 HIS cc_start: 0.7817 (m90) cc_final: 0.7532 (m170) REVERT: P 58 PHE cc_start: 0.9493 (p90) cc_final: 0.9285 (p90) REVERT: Q 72 ASN cc_start: 0.8462 (m-40) cc_final: 0.8120 (m-40) REVERT: R 65 VAL cc_start: 0.7803 (t) cc_final: 0.7219 (p) REVERT: S 16 LYS cc_start: 0.8767 (pttt) cc_final: 0.8287 (pttm) REVERT: S 93 LYS cc_start: 0.8071 (pttt) cc_final: 0.7382 (pttt) REVERT: S 94 ARG cc_start: 0.7229 (mmt-90) cc_final: 0.6802 (mmp80) REVERT: T 83 ILE cc_start: 0.9304 (mt) cc_final: 0.9016 (mm) REVERT: V 15 THR cc_start: 0.8388 (m) cc_final: 0.8159 (p) REVERT: W 32 LYS cc_start: 0.8107 (mttt) cc_final: 0.7585 (mtmm) outliers start: 0 outliers final: 0 residues processed: 883 average time/residue: 1.1087 time to fit residues: 1534.4729 Evaluate side-chains 646 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 646 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 532 optimal weight: 9.9990 chunk 478 optimal weight: 0.9980 chunk 265 optimal weight: 50.0000 chunk 163 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 494 optimal weight: 0.6980 chunk 191 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 368 optimal weight: 1.9990 chunk 573 optimal weight: 0.7980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 51 HIS 3 53 ASN 3 63 ASN C 76 ASN C 227 ASN C 233 HIS D 51 GLN D 76 ASN D 135 GLN D 145 HIS D 179 ASN D 183 HIS J 147 GLN K 4 GLN M 123 HIS N 107 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN Q 77 ASN Q 94 ASN R 68 HIS R 93 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 58 HIS V 62 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 102983 Z= 0.191 Angle : 0.589 10.329 155232 Z= 0.297 Chirality : 0.032 0.285 19969 Planarity : 0.005 0.060 7675 Dihedral : 23.026 178.669 54354 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.91 % Favored : 92.84 % Rotamer: Outliers : 2.27 % Allowed : 9.93 % Favored : 87.79 % 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: -1.60 (0.14), residues: 3156 helix: 0.41 (0.18), residues: 766 sheet: -1.10 (0.22), residues: 511 loop : -1.76 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 15 HIS 0.010 0.001 HIS P 76 PHE 0.023 0.002 PHE Y 30 TYR 0.021 0.002 TYR P 65 ARG 0.009 0.001 ARG S 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 735 time to evaluate : 3.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 8 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8183 (tttp) REVERT: 1 53 GLU cc_start: 0.7715 (mp0) cc_final: 0.7187 (mp0) REVERT: 2 21 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6938 (p90) REVERT: 3 30 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7496 (mtp85) REVERT: 3 59 THR cc_start: 0.7399 (p) cc_final: 0.7184 (p) REVERT: 4 19 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7916 (ttp-110) REVERT: 4 24 MET cc_start: 0.7316 (ptp) cc_final: 0.6921 (ptp) REVERT: C 25 THR cc_start: 0.7920 (m) cc_final: 0.7591 (t) REVERT: C 78 LYS cc_start: 0.8048 (tttt) cc_final: 0.7559 (tptm) REVERT: C 84 TYR cc_start: 0.7943 (t80) cc_final: 0.7587 (t80) REVERT: C 155 LEU cc_start: 0.8616 (tp) cc_final: 0.8396 (tp) REVERT: C 192 THR cc_start: 0.8440 (m) cc_final: 0.8154 (p) REVERT: C 225 VAL cc_start: 0.9120 (m) cc_final: 0.8683 (p) REVERT: D 14 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8444 (p) REVERT: D 24 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9069 (t) REVERT: E 70 LYS cc_start: 0.6322 (mttt) cc_final: 0.5740 (mttt) REVERT: E 129 ARG cc_start: 0.8340 (mmt180) cc_final: 0.7906 (mmm160) REVERT: E 173 LYS cc_start: 0.7547 (mmtm) cc_final: 0.7295 (mmtm) REVERT: F 84 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.5108 (p90) REVERT: F 109 ARG cc_start: 0.6390 (mtm180) cc_final: 0.6181 (mtm180) REVERT: J 53 PHE cc_start: 0.8250 (m-10) cc_final: 0.7931 (m-80) REVERT: J 58 ASN cc_start: 0.6958 (t0) cc_final: 0.6588 (t0) REVERT: K 9 LYS cc_start: 0.8334 (mttt) cc_final: 0.8041 (mttm) REVERT: K 53 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7396 (mmtm) REVERT: K 64 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7559 (mtm-85) REVERT: L 8 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8486 (mp) REVERT: L 49 PHE cc_start: 0.7833 (t80) cc_final: 0.7461 (t80) REVERT: L 116 LYS cc_start: 0.7910 (tttt) cc_final: 0.7599 (tttp) REVERT: M 83 MET cc_start: 0.7268 (mmm) cc_final: 0.6956 (mmp) REVERT: N 74 ASP cc_start: 0.7550 (p0) cc_final: 0.7333 (p0) REVERT: O 17 HIS cc_start: 0.7452 (t-90) cc_final: 0.7101 (t-90) REVERT: O 79 VAL cc_start: 0.8649 (t) cc_final: 0.8227 (t) REVERT: P 25 ILE cc_start: 0.9210 (mt) cc_final: 0.8923 (mp) REVERT: P 45 VAL cc_start: 0.8769 (t) cc_final: 0.8349 (p) REVERT: R 70 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7416 (mtmt) REVERT: S 16 LYS cc_start: 0.8972 (pttt) cc_final: 0.8550 (pttm) REVERT: S 102 ARG cc_start: 0.7188 (mmm160) cc_final: 0.6841 (mmt180) REVERT: S 118 GLU cc_start: 0.5708 (tp30) cc_final: 0.4811 (tp30) REVERT: T 34 ARG cc_start: 0.7432 (ttp-170) cc_final: 0.7203 (ttm110) REVERT: T 73 TYR cc_start: 0.7210 (m-80) cc_final: 0.6819 (m-10) REVERT: T 83 ILE cc_start: 0.9312 (mt) cc_final: 0.8639 (tt) REVERT: U 97 ILE cc_start: 0.8435 (pt) cc_final: 0.8084 (tt) REVERT: V 15 THR cc_start: 0.8417 (m) cc_final: 0.8154 (p) REVERT: W 20 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7236 (mmm-85) REVERT: W 32 LYS cc_start: 0.8289 (mttt) cc_final: 0.7688 (mtmm) REVERT: W 41 ARG cc_start: 0.8548 (ptp-110) cc_final: 0.8213 (ptp90) REVERT: X 22 HIS cc_start: 0.8567 (t70) cc_final: 0.8254 (t70) REVERT: X 28 ARG cc_start: 0.8052 (ptm-80) cc_final: 0.7315 (ptm-80) REVERT: Y 21 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8150 (mmm-85) REVERT: Z 55 GLU cc_start: 0.6871 (tt0) cc_final: 0.6657 (tt0) outliers start: 59 outliers final: 31 residues processed: 756 average time/residue: 1.0843 time to fit residues: 1325.9723 Evaluate side-chains 700 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 664 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain S residue 71 ASN Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 40 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 318 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 476 optimal weight: 20.0000 chunk 390 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 574 optimal weight: 10.0000 chunk 620 optimal weight: 6.9990 chunk 511 optimal weight: 7.9990 chunk 569 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 460 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS 1 20 HIS 1 44 ASN C 76 ASN D 183 HIS E 140 GLN E 188 GLN F 26 GLN G 7 GLN G 144 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 GLN M 67 ASN M 123 HIS N 107 ASN ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 74 GLN W 29 GLN X 32 ASN X 37 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 102983 Z= 0.438 Angle : 0.822 11.646 155232 Z= 0.407 Chirality : 0.042 0.398 19969 Planarity : 0.007 0.067 7675 Dihedral : 23.379 179.003 54354 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.85 % Favored : 89.83 % Rotamer: Outliers : 4.74 % Allowed : 12.32 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.14), residues: 3156 helix: -0.41 (0.17), residues: 780 sheet: -1.16 (0.21), residues: 517 loop : -2.08 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 206 HIS 0.037 0.003 HIS R 68 PHE 0.033 0.003 PHE N 80 TYR 0.022 0.003 TYR K 76 ARG 0.021 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 802 time to evaluate : 3.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 23 TYR cc_start: 0.8242 (m-10) cc_final: 0.7984 (m-10) REVERT: 1 29 ARG cc_start: 0.7383 (mmp80) cc_final: 0.7016 (mtt-85) REVERT: 1 40 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8099 (mtpp) REVERT: 1 53 GLU cc_start: 0.7841 (mp0) cc_final: 0.7201 (mp0) REVERT: 2 9 GLN cc_start: 0.8161 (tp40) cc_final: 0.7928 (mt0) REVERT: 2 23 LEU cc_start: 0.8893 (tp) cc_final: 0.8566 (tp) REVERT: 2 39 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7823 (ttp-110) REVERT: 2 40 LYS cc_start: 0.8401 (tttt) cc_final: 0.8198 (ttpt) REVERT: C 62 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.7807 (p90) REVERT: C 78 LYS cc_start: 0.8320 (tttt) cc_final: 0.7772 (tptm) REVERT: C 95 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8557 (pp) REVERT: C 175 LEU cc_start: 0.9213 (mt) cc_final: 0.9005 (mt) REVERT: C 192 THR cc_start: 0.8640 (m) cc_final: 0.8319 (p) REVERT: C 225 VAL cc_start: 0.9272 (m) cc_final: 0.8898 (p) REVERT: D 14 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8464 (p) REVERT: D 62 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8535 (m) REVERT: D 76 ASN cc_start: 0.7883 (t0) cc_final: 0.7602 (m-40) REVERT: E 70 LYS cc_start: 0.7036 (mttt) cc_final: 0.6405 (ttpp) REVERT: E 173 LYS cc_start: 0.7596 (mmtm) cc_final: 0.7348 (mmtm) REVERT: E 189 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8289 (tt) REVERT: F 84 PHE cc_start: 0.5150 (OUTLIER) cc_final: 0.4725 (p90) REVERT: F 109 ARG cc_start: 0.6403 (mtm180) cc_final: 0.6025 (mtm180) REVERT: J 58 ASN cc_start: 0.7707 (t0) cc_final: 0.7437 (t0) REVERT: J 86 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8558 (ttpp) REVERT: J 89 ILE cc_start: 0.8389 (tt) cc_final: 0.7938 (tt) REVERT: J 119 GLN cc_start: 0.8177 (tt0) cc_final: 0.7865 (tm-30) REVERT: J 132 HIS cc_start: 0.7070 (m-70) cc_final: 0.6162 (m-70) REVERT: K 3 GLN cc_start: 0.7982 (pt0) cc_final: 0.7722 (pt0) REVERT: K 23 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7918 (mmm160) REVERT: K 53 LYS cc_start: 0.7843 (mmtt) cc_final: 0.7569 (mmtm) REVERT: M 131 ILE cc_start: 0.8816 (pt) cc_final: 0.8334 (mp) REVERT: O 13 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7605 (ttp80) REVERT: O 102 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: P 45 VAL cc_start: 0.8903 (t) cc_final: 0.8695 (p) REVERT: P 65 TYR cc_start: 0.8661 (m-80) cc_final: 0.8430 (m-80) REVERT: P 77 SER cc_start: 0.8665 (t) cc_final: 0.8463 (t) REVERT: Q 84 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8369 (mmmm) REVERT: Q 95 LEU cc_start: 0.9114 (tp) cc_final: 0.8887 (tp) REVERT: R 24 LYS cc_start: 0.8532 (mtpp) cc_final: 0.7974 (mtpp) REVERT: R 65 VAL cc_start: 0.7835 (t) cc_final: 0.7558 (p) REVERT: S 16 LYS cc_start: 0.9060 (pttt) cc_final: 0.8642 (pttm) REVERT: S 85 TYR cc_start: 0.7718 (m-80) cc_final: 0.7462 (m-80) REVERT: S 118 GLU cc_start: 0.5992 (tp30) cc_final: 0.4969 (tp30) REVERT: T 28 VAL cc_start: 0.8421 (t) cc_final: 0.8082 (m) REVERT: T 34 ARG cc_start: 0.7565 (ttp-170) cc_final: 0.7300 (ttp-110) REVERT: T 83 ILE cc_start: 0.9431 (mt) cc_final: 0.8767 (tt) REVERT: V 96 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6824 (tp) REVERT: W 15 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: W 32 LYS cc_start: 0.8516 (mttt) cc_final: 0.7868 (mtmm) REVERT: X 26 SER cc_start: 0.8542 (m) cc_final: 0.8326 (m) REVERT: X 28 ARG cc_start: 0.8310 (ptm-80) cc_final: 0.7751 (ptm-80) REVERT: Y 9 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7048 (mp0) REVERT: Y 12 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8139 (tm-30) REVERT: Y 46 ARG cc_start: 0.6367 (ptp-170) cc_final: 0.6068 (ptp-170) REVERT: Y 49 THR cc_start: 0.8617 (m) cc_final: 0.8416 (p) outliers start: 123 outliers final: 81 residues processed: 848 average time/residue: 1.0721 time to fit residues: 1482.4101 Evaluate side-chains 843 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 753 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 21 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 16 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 64 ASP Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 71 ASN Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 45 ASN Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 40 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 567 optimal weight: 8.9990 chunk 431 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 chunk 576 optimal weight: 20.0000 chunk 609 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 546 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS N 23 ASN ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 118 ASN P 26 ASN ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 102983 Z= 0.256 Angle : 0.616 11.024 155232 Z= 0.315 Chirality : 0.035 0.373 19969 Planarity : 0.005 0.070 7675 Dihedral : 23.304 179.137 54354 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.38 % Favored : 92.36 % Rotamer: Outliers : 4.70 % Allowed : 15.98 % Favored : 79.32 % 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: -2.06 (0.14), residues: 3156 helix: 0.05 (0.19), residues: 774 sheet: -1.28 (0.21), residues: 540 loop : -2.11 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 250 HIS 0.017 0.001 HIS R 77 PHE 0.022 0.002 PHE N 29 TYR 0.015 0.002 TYR F 15 ARG 0.014 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 775 time to evaluate : 3.845 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6480 (ttp80) REVERT: 1 29 ARG cc_start: 0.7328 (mmp80) cc_final: 0.6868 (mtt90) REVERT: 2 9 GLN cc_start: 0.8472 (tp40) cc_final: 0.8141 (mt0) REVERT: 2 23 LEU cc_start: 0.8600 (tp) cc_final: 0.8381 (tt) REVERT: 3 7 HIS cc_start: 0.7381 (t-90) cc_final: 0.7120 (t-90) REVERT: C 62 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7615 (p90) REVERT: C 78 LYS cc_start: 0.8291 (tttt) cc_final: 0.7758 (tptm) REVERT: C 104 TYR cc_start: 0.8758 (m-80) cc_final: 0.8448 (m-80) REVERT: C 119 SER cc_start: 0.8011 (t) cc_final: 0.7736 (t) REVERT: C 192 THR cc_start: 0.8668 (m) cc_final: 0.8341 (p) REVERT: C 225 VAL cc_start: 0.9122 (m) cc_final: 0.8743 (t) REVERT: D 14 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8448 (p) REVERT: D 76 ASN cc_start: 0.7939 (t0) cc_final: 0.7600 (m-40) REVERT: E 121 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8739 (mm) REVERT: E 192 TYR cc_start: 0.8594 (t80) cc_final: 0.8299 (t80) REVERT: F 84 PHE cc_start: 0.5334 (OUTLIER) cc_final: 0.4722 (p90) REVERT: G 138 ASP cc_start: 0.6277 (t0) cc_final: 0.5366 (p0) REVERT: H 22 LYS cc_start: 0.7151 (ptmt) cc_final: 0.6850 (ptmm) REVERT: J 27 ARG cc_start: 0.7168 (mtm110) cc_final: 0.6757 (mtp180) REVERT: J 58 ASN cc_start: 0.7799 (t0) cc_final: 0.7506 (t0) REVERT: J 86 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8407 (ttpp) REVERT: J 89 ILE cc_start: 0.8139 (tt) cc_final: 0.7752 (tt) REVERT: J 119 GLN cc_start: 0.8151 (tt0) cc_final: 0.7857 (tm-30) REVERT: K 9 LYS cc_start: 0.8257 (mttt) cc_final: 0.8041 (mttt) REVERT: K 53 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7551 (mmtm) REVERT: K 106 LEU cc_start: 0.6926 (mm) cc_final: 0.5907 (pp) REVERT: L 49 PHE cc_start: 0.8318 (t80) cc_final: 0.7820 (t80) REVERT: M 131 ILE cc_start: 0.8610 (pt) cc_final: 0.8299 (mp) REVERT: N 60 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8912 (tp) REVERT: O 13 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7686 (mtp180) REVERT: Q 24 TYR cc_start: 0.8751 (m-10) cc_final: 0.8478 (m-10) REVERT: S 59 LYS cc_start: 0.8453 (mttt) cc_final: 0.8243 (mttt) REVERT: S 85 TYR cc_start: 0.7593 (m-80) cc_final: 0.7304 (m-80) REVERT: S 118 GLU cc_start: 0.5863 (tp30) cc_final: 0.4864 (tp30) REVERT: T 34 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.7188 (ttm110) REVERT: T 83 ILE cc_start: 0.9453 (mt) cc_final: 0.9008 (tt) REVERT: U 22 LYS cc_start: 0.8128 (tptp) cc_final: 0.7921 (tptp) REVERT: U 42 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7542 (mtmm) REVERT: V 96 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7027 (tp) REVERT: W 32 LYS cc_start: 0.8599 (mttt) cc_final: 0.7880 (mtmm) REVERT: X 28 ARG cc_start: 0.8318 (ptm-80) cc_final: 0.7579 (ptm-80) REVERT: X 51 VAL cc_start: 0.9157 (p) cc_final: 0.8842 (t) REVERT: Y 12 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8038 (tm-30) REVERT: Y 21 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8288 (mmm-85) REVERT: Y 31 ASN cc_start: 0.8300 (m-40) cc_final: 0.7843 (t0) REVERT: Y 49 THR cc_start: 0.8571 (m) cc_final: 0.8347 (p) REVERT: Z 57 GLU cc_start: 0.8435 (mp0) cc_final: 0.8154 (mp0) outliers start: 122 outliers final: 86 residues processed: 822 average time/residue: 1.0142 time to fit residues: 1359.5892 Evaluate side-chains 809 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 716 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 0 residue 41 ARG Chi-restraints excluded: chain 2 residue 21 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 135 GLN Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 122 PHE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 71 ASN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 73 TYR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 507 optimal weight: 0.0570 chunk 346 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 454 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 520 optimal weight: 7.9990 chunk 421 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 547 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 overall best weight: 6.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 145 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 ASN M 123 HIS N 62 ASN ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN R 91 HIS ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 GLN ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 GLN ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 102983 Z= 0.349 Angle : 0.696 11.478 155232 Z= 0.350 Chirality : 0.038 0.407 19969 Planarity : 0.006 0.069 7675 Dihedral : 23.392 179.999 54354 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.20 % Favored : 89.54 % Rotamer: Outliers : 6.35 % Allowed : 16.60 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.14), residues: 3156 helix: -0.04 (0.19), residues: 772 sheet: -1.37 (0.21), residues: 532 loop : -2.22 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 92 HIS 0.018 0.002 HIS R 77 PHE 0.020 0.002 PHE Y 30 TYR 0.018 0.002 TYR M 32 ARG 0.014 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 753 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.6543 (ttp80) REVERT: 1 29 ARG cc_start: 0.7251 (mmp80) cc_final: 0.6749 (mtt90) REVERT: 2 9 GLN cc_start: 0.8608 (tp40) cc_final: 0.8114 (mt0) REVERT: 2 28 ARG cc_start: 0.8704 (ttm-80) cc_final: 0.8487 (ttm170) REVERT: C 62 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7670 (p90) REVERT: C 95 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8409 (pp) REVERT: C 104 TYR cc_start: 0.8820 (m-80) cc_final: 0.8574 (m-80) REVERT: C 119 SER cc_start: 0.8206 (t) cc_final: 0.7924 (t) REVERT: C 192 THR cc_start: 0.8683 (m) cc_final: 0.8391 (p) REVERT: C 225 VAL cc_start: 0.9015 (m) cc_final: 0.8649 (t) REVERT: D 14 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8432 (p) REVERT: D 15 GLN cc_start: 0.8466 (pt0) cc_final: 0.8079 (pt0) REVERT: D 76 ASN cc_start: 0.7903 (t0) cc_final: 0.7525 (m-40) REVERT: D 83 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7099 (mt-10) REVERT: E 121 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8718 (mm) REVERT: E 189 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8331 (tt) REVERT: F 64 LEU cc_start: 0.8528 (mt) cc_final: 0.7918 (mp) REVERT: F 84 PHE cc_start: 0.5354 (OUTLIER) cc_final: 0.4754 (p90) REVERT: G 138 ASP cc_start: 0.6294 (t0) cc_final: 0.5605 (p0) REVERT: J 27 ARG cc_start: 0.7138 (mtm110) cc_final: 0.6874 (mtp180) REVERT: J 58 ASN cc_start: 0.7972 (t0) cc_final: 0.6797 (t0) REVERT: J 89 ILE cc_start: 0.8356 (tt) cc_final: 0.7823 (tt) REVERT: J 94 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: J 119 GLN cc_start: 0.8275 (tt0) cc_final: 0.7963 (tm-30) REVERT: K 30 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8645 (ttt90) REVERT: K 53 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7562 (mmtm) REVERT: L 20 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7898 (mtm110) REVERT: M 130 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.7937 (mtm-85) REVERT: M 131 ILE cc_start: 0.8763 (pt) cc_final: 0.8359 (mp) REVERT: N 60 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8920 (tp) REVERT: O 55 VAL cc_start: 0.7296 (m) cc_final: 0.7016 (p) REVERT: P 88 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.6976 (mmm160) REVERT: Q 24 TYR cc_start: 0.8758 (m-10) cc_final: 0.8522 (m-10) REVERT: R 26 GLU cc_start: 0.6111 (mm-30) cc_final: 0.5872 (mm-30) REVERT: S 59 LYS cc_start: 0.8428 (mttt) cc_final: 0.8119 (mttt) REVERT: S 85 TYR cc_start: 0.7757 (m-80) cc_final: 0.7444 (m-80) REVERT: S 118 GLU cc_start: 0.5971 (tp30) cc_final: 0.4910 (tp30) REVERT: T 34 ARG cc_start: 0.7321 (ttp-170) cc_final: 0.7062 (ttp-110) REVERT: T 83 ILE cc_start: 0.9491 (mt) cc_final: 0.8926 (tt) REVERT: U 22 LYS cc_start: 0.8370 (tptp) cc_final: 0.8138 (tptp) REVERT: U 31 ASN cc_start: 0.8876 (m-40) cc_final: 0.8645 (m-40) REVERT: U 42 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7410 (mtmm) REVERT: U 62 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6879 (mm110) REVERT: V 96 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7237 (tp) REVERT: W 32 LYS cc_start: 0.8695 (mttt) cc_final: 0.7982 (mtmm) REVERT: X 28 ARG cc_start: 0.8351 (ptm-80) cc_final: 0.7916 (ptm-80) REVERT: Y 12 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8092 (tm-30) REVERT: Y 21 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8210 (mmm-85) REVERT: Y 31 ASN cc_start: 0.8393 (m-40) cc_final: 0.7896 (t0) REVERT: Y 49 THR cc_start: 0.8569 (m) cc_final: 0.8343 (p) outliers start: 165 outliers final: 122 residues processed: 824 average time/residue: 1.0238 time to fit residues: 1370.9853 Evaluate side-chains 857 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 723 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 0 residue 41 ARG Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 21 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 135 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 20 ARG Chi-restraints excluded: chain L residue 25 ASP Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 73 TYR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 47 LEU Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain W residue 15 ASP Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain Y residue 46 ARG Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 205 optimal weight: 10.0000 chunk 549 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 358 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 610 optimal weight: 5.9990 chunk 506 optimal weight: 0.0030 chunk 282 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 201 optimal weight: 20.0000 chunk 320 optimal weight: 8.9990 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 GLN ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 102983 Z= 0.278 Angle : 0.629 11.110 155232 Z= 0.320 Chirality : 0.036 0.403 19969 Planarity : 0.005 0.068 7675 Dihedral : 23.412 179.518 54354 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.71 % Favored : 91.03 % Rotamer: Outliers : 5.93 % Allowed : 18.14 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.14), residues: 3156 helix: 0.04 (0.19), residues: 773 sheet: -1.28 (0.21), residues: 531 loop : -2.21 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 250 HIS 0.019 0.001 HIS V 44 PHE 0.015 0.002 PHE N 29 TYR 0.036 0.002 TYR 1 23 ARG 0.011 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 753 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.6822 (ttp80) REVERT: 1 29 ARG cc_start: 0.7062 (mmp80) cc_final: 0.6543 (mtt90) REVERT: 1 53 GLU cc_start: 0.8006 (mp0) cc_final: 0.7790 (mp0) REVERT: 2 9 GLN cc_start: 0.8537 (tp40) cc_final: 0.8089 (mt0) REVERT: 2 28 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8390 (ttm170) REVERT: 2 39 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7849 (ttp-110) REVERT: C 62 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7492 (p90) REVERT: C 95 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8341 (pp) REVERT: C 119 SER cc_start: 0.8172 (t) cc_final: 0.7884 (t) REVERT: C 192 THR cc_start: 0.8631 (m) cc_final: 0.8330 (p) REVERT: C 225 VAL cc_start: 0.8994 (m) cc_final: 0.8600 (t) REVERT: D 14 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8441 (p) REVERT: D 132 PHE cc_start: 0.8599 (m-10) cc_final: 0.8321 (m-80) REVERT: E 121 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8736 (mm) REVERT: E 189 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8370 (tt) REVERT: E 192 TYR cc_start: 0.8624 (t80) cc_final: 0.8275 (t80) REVERT: E 196 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7482 (ttm170) REVERT: F 12 LYS cc_start: 0.5522 (OUTLIER) cc_final: 0.4754 (ptpp) REVERT: F 84 PHE cc_start: 0.5338 (OUTLIER) cc_final: 0.4688 (p90) REVERT: G 63 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.5094 (ptp90) REVERT: G 138 ASP cc_start: 0.6156 (t0) cc_final: 0.5634 (p0) REVERT: G 141 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8301 (mmmm) REVERT: G 173 LYS cc_start: 0.6816 (ttpt) cc_final: 0.6314 (ttpt) REVERT: J 27 ARG cc_start: 0.7035 (mtm110) cc_final: 0.6723 (mtp180) REVERT: J 53 PHE cc_start: 0.8433 (m-80) cc_final: 0.8211 (m-80) REVERT: J 58 ASN cc_start: 0.7844 (t0) cc_final: 0.7117 (t0) REVERT: J 89 ILE cc_start: 0.8256 (tt) cc_final: 0.7801 (tt) REVERT: J 119 GLN cc_start: 0.8308 (tt0) cc_final: 0.7992 (tm-30) REVERT: K 9 LYS cc_start: 0.8178 (mttt) cc_final: 0.7676 (mttt) REVERT: K 30 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8641 (ttt90) REVERT: K 53 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7549 (mmtm) REVERT: K 65 THR cc_start: 0.9199 (m) cc_final: 0.8894 (p) REVERT: L 126 HIS cc_start: 0.7115 (m90) cc_final: 0.6678 (m90) REVERT: L 127 LYS cc_start: 0.7969 (mmtm) cc_final: 0.7719 (mmtm) REVERT: M 130 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7832 (mtm-85) REVERT: M 131 ILE cc_start: 0.8544 (pt) cc_final: 0.8274 (mp) REVERT: M 134 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5048 (mtp180) REVERT: N 60 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8923 (tp) REVERT: N 117 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.5501 (mpt180) REVERT: O 55 VAL cc_start: 0.7208 (m) cc_final: 0.6922 (p) REVERT: P 23 ASP cc_start: 0.7062 (m-30) cc_final: 0.6446 (m-30) REVERT: P 88 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.6987 (mmm160) REVERT: P 97 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: R 26 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5810 (mm-30) REVERT: S 59 LYS cc_start: 0.8451 (mttt) cc_final: 0.8232 (mttt) REVERT: S 118 GLU cc_start: 0.6181 (tp30) cc_final: 0.5030 (tp30) REVERT: T 34 ARG cc_start: 0.7315 (ttp-170) cc_final: 0.7034 (ttm110) REVERT: T 41 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: T 83 ILE cc_start: 0.9480 (mt) cc_final: 0.8986 (tt) REVERT: U 22 LYS cc_start: 0.8335 (tptp) cc_final: 0.8046 (tptp) REVERT: U 42 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7594 (mtmm) REVERT: U 62 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7167 (mm110) REVERT: U 93 LYS cc_start: 0.7704 (tttt) cc_final: 0.7383 (ttmm) REVERT: V 75 LEU cc_start: 0.7792 (mm) cc_final: 0.7522 (mt) REVERT: V 96 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7230 (tp) REVERT: W 32 LYS cc_start: 0.8656 (mttt) cc_final: 0.7956 (mtmm) REVERT: X 28 ARG cc_start: 0.8336 (ptm-80) cc_final: 0.7603 (ptm-80) REVERT: Y 31 ASN cc_start: 0.8397 (m-40) cc_final: 0.7987 (t0) outliers start: 154 outliers final: 111 residues processed: 822 average time/residue: 1.0536 time to fit residues: 1422.3753 Evaluate side-chains 853 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 726 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 41 ARG Chi-restraints excluded: chain 2 residue 21 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 86 LYS Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 41 GLN Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 73 TYR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 47 LEU Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 40 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 588 optimal weight: 0.0040 chunk 68 optimal weight: 10.0000 chunk 347 optimal weight: 20.0000 chunk 445 optimal weight: 0.0970 chunk 345 optimal weight: 10.0000 chunk 513 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 608 optimal weight: 10.0000 chunk 380 optimal weight: 0.8980 chunk 370 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN M 123 HIS N 62 ASN ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 GLN ** U 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 102983 Z= 0.212 Angle : 0.573 10.457 155232 Z= 0.293 Chirality : 0.033 0.397 19969 Planarity : 0.005 0.055 7675 Dihedral : 23.380 179.907 54354 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.65 % Favored : 91.16 % Rotamer: Outliers : 5.51 % Allowed : 19.56 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3156 helix: 0.24 (0.19), residues: 760 sheet: -1.08 (0.22), residues: 512 loop : -2.16 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 250 HIS 0.012 0.001 HIS V 44 PHE 0.018 0.002 PHE K 111 TYR 0.016 0.002 TYR O 102 ARG 0.015 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 750 time to evaluate : 3.807 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: 1 16 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7765 (mp0) REVERT: 1 29 ARG cc_start: 0.7076 (mmp80) cc_final: 0.6674 (mtt90) REVERT: 1 53 GLU cc_start: 0.8000 (mp0) cc_final: 0.7790 (mp0) REVERT: 2 9 GLN cc_start: 0.8515 (tp40) cc_final: 0.8099 (mt0) REVERT: 2 28 ARG cc_start: 0.8579 (ttm-80) cc_final: 0.8369 (ttm170) REVERT: 3 3 LYS cc_start: 0.8113 (tttt) cc_final: 0.7867 (tttt) REVERT: 3 58 VAL cc_start: 0.8764 (t) cc_final: 0.8542 (t) REVERT: C 95 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8396 (pp) REVERT: C 119 SER cc_start: 0.8129 (t) cc_final: 0.7844 (t) REVERT: C 192 THR cc_start: 0.8587 (m) cc_final: 0.8307 (p) REVERT: C 225 VAL cc_start: 0.8888 (m) cc_final: 0.8505 (t) REVERT: C 226 MET cc_start: 0.8088 (mtt) cc_final: 0.7871 (mtp) REVERT: D 14 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8403 (p) REVERT: D 209 ARG cc_start: 0.8849 (ptp-170) cc_final: 0.8451 (mtp180) REVERT: E 121 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8748 (mm) REVERT: E 192 TYR cc_start: 0.8620 (t80) cc_final: 0.8164 (t80) REVERT: E 196 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7542 (ttm170) REVERT: F 84 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.4581 (p90) REVERT: F 159 MET cc_start: 0.6134 (pmm) cc_final: 0.5717 (pmm) REVERT: G 138 ASP cc_start: 0.6074 (t0) cc_final: 0.5551 (p0) REVERT: G 139 LYS cc_start: 0.7405 (mttp) cc_final: 0.7143 (mttp) REVERT: G 173 LYS cc_start: 0.6791 (ttpt) cc_final: 0.6305 (ttpt) REVERT: J 27 ARG cc_start: 0.6983 (mtm110) cc_final: 0.6543 (mtp180) REVERT: J 53 PHE cc_start: 0.8471 (m-80) cc_final: 0.8244 (m-80) REVERT: J 58 ASN cc_start: 0.7605 (t0) cc_final: 0.7126 (t0) REVERT: J 89 ILE cc_start: 0.8084 (tt) cc_final: 0.7629 (tt) REVERT: J 119 GLN cc_start: 0.8319 (tt0) cc_final: 0.7994 (tm-30) REVERT: K 9 LYS cc_start: 0.8155 (mttt) cc_final: 0.7676 (mttt) REVERT: K 30 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8472 (ttt90) REVERT: K 53 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7634 (mmtm) REVERT: K 65 THR cc_start: 0.9191 (m) cc_final: 0.8921 (p) REVERT: L 126 HIS cc_start: 0.6801 (m90) cc_final: 0.6218 (m90) REVERT: L 127 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7922 (mmtm) REVERT: M 134 ARG cc_start: 0.5657 (OUTLIER) cc_final: 0.4912 (mtp180) REVERT: N 60 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8934 (tp) REVERT: N 117 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.5269 (mpt180) REVERT: O 23 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7694 (tptp) REVERT: O 55 VAL cc_start: 0.7313 (m) cc_final: 0.7039 (p) REVERT: P 23 ASP cc_start: 0.7154 (m-30) cc_final: 0.6815 (m-30) REVERT: P 97 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.7792 (m-10) REVERT: Q 106 PHE cc_start: 0.8464 (t80) cc_final: 0.8239 (t80) REVERT: R 26 GLU cc_start: 0.5962 (mm-30) cc_final: 0.5729 (mm-30) REVERT: S 59 LYS cc_start: 0.8518 (mttt) cc_final: 0.8277 (mttt) REVERT: S 118 GLU cc_start: 0.5921 (tp30) cc_final: 0.4918 (tp30) REVERT: T 34 ARG cc_start: 0.7279 (ttp-170) cc_final: 0.6983 (ttm110) REVERT: T 83 ILE cc_start: 0.9467 (mt) cc_final: 0.8989 (tt) REVERT: U 22 LYS cc_start: 0.8199 (tptp) cc_final: 0.7931 (tptp) REVERT: U 42 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7589 (mtmm) REVERT: U 93 LYS cc_start: 0.7435 (tttt) cc_final: 0.7155 (ttmm) REVERT: V 96 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7250 (tp) REVERT: W 32 LYS cc_start: 0.8648 (mttt) cc_final: 0.8035 (mtmm) REVERT: X 28 ARG cc_start: 0.8372 (ptm-80) cc_final: 0.7704 (ptm-80) REVERT: Y 31 ASN cc_start: 0.8367 (m-40) cc_final: 0.7993 (t0) REVERT: Z 29 ARG cc_start: 0.7453 (mmt90) cc_final: 0.7252 (mmt90) outliers start: 143 outliers final: 111 residues processed: 811 average time/residue: 0.9997 time to fit residues: 1326.3593 Evaluate side-chains 842 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 721 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 2 residue 21 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 73 TYR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 47 LEU Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 40 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 376 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 414 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 478 optimal weight: 0.5980 overall best weight: 7.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 20 ASN C 76 ASN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 102983 Z= 0.415 Angle : 0.762 10.758 155232 Z= 0.378 Chirality : 0.040 0.450 19969 Planarity : 0.006 0.089 7675 Dihedral : 23.573 179.765 54354 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.19 % Favored : 88.56 % Rotamer: Outliers : 6.16 % Allowed : 19.60 % Favored : 74.24 % 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: -2.37 (0.14), residues: 3156 helix: -0.15 (0.19), residues: 761 sheet: -1.43 (0.22), residues: 533 loop : -2.33 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP M 92 HIS 0.016 0.002 HIS D 130 PHE 0.024 0.002 PHE D 132 TYR 0.036 0.003 TYR 1 23 ARG 0.016 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 733 time to evaluate : 3.861 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: 0 8 LYS cc_start: 0.8887 (tttp) cc_final: 0.8673 (mttp) REVERT: 1 16 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7708 (mp0) REVERT: 2 9 GLN cc_start: 0.8616 (tp40) cc_final: 0.8068 (mt0) REVERT: 2 28 ARG cc_start: 0.8710 (ttm-80) cc_final: 0.8489 (ttm170) REVERT: 3 58 VAL cc_start: 0.8696 (t) cc_final: 0.8482 (t) REVERT: C 52 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7905 (mtm-85) REVERT: C 62 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.8022 (p90) REVERT: C 95 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8483 (pp) REVERT: C 119 SER cc_start: 0.8512 (t) cc_final: 0.8196 (t) REVERT: C 181 GLU cc_start: 0.7595 (tt0) cc_final: 0.7389 (tt0) REVERT: C 192 THR cc_start: 0.8810 (m) cc_final: 0.8488 (p) REVERT: C 225 VAL cc_start: 0.8977 (m) cc_final: 0.8553 (t) REVERT: D 15 GLN cc_start: 0.8602 (pt0) cc_final: 0.8356 (pt0) REVERT: D 54 TYR cc_start: 0.8764 (t80) cc_final: 0.8244 (t80) REVERT: E 121 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8896 (mm) REVERT: F 12 LYS cc_start: 0.5399 (OUTLIER) cc_final: 0.4555 (ptpp) REVERT: F 84 PHE cc_start: 0.5409 (OUTLIER) cc_final: 0.4764 (p90) REVERT: J 53 PHE cc_start: 0.8531 (m-80) cc_final: 0.8312 (m-80) REVERT: J 58 ASN cc_start: 0.8034 (t0) cc_final: 0.7612 (t0) REVERT: J 86 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8519 (ttpp) REVERT: J 89 ILE cc_start: 0.8317 (tt) cc_final: 0.7873 (tt) REVERT: J 119 GLN cc_start: 0.8411 (tt0) cc_final: 0.8135 (tm-30) REVERT: K 9 LYS cc_start: 0.8162 (mttt) cc_final: 0.7681 (mttt) REVERT: K 30 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8656 (ttt90) REVERT: K 53 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7508 (mmtm) REVERT: K 65 THR cc_start: 0.9194 (m) cc_final: 0.8955 (p) REVERT: L 127 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7759 (mmtm) REVERT: M 130 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8066 (mtm-85) REVERT: M 131 ILE cc_start: 0.8662 (mp) cc_final: 0.8315 (mp) REVERT: M 134 ARG cc_start: 0.5516 (OUTLIER) cc_final: 0.5198 (mtp180) REVERT: N 60 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8962 (tp) REVERT: O 55 VAL cc_start: 0.7173 (m) cc_final: 0.6884 (p) REVERT: P 97 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7999 (m-10) REVERT: S 59 LYS cc_start: 0.8514 (mttt) cc_final: 0.8218 (mttt) REVERT: S 102 ARG cc_start: 0.7222 (mtp180) cc_final: 0.6958 (mtm-85) REVERT: S 118 GLU cc_start: 0.5621 (tp30) cc_final: 0.4618 (tp30) REVERT: T 34 ARG cc_start: 0.7348 (ttp-170) cc_final: 0.7067 (ttm110) REVERT: T 83 ILE cc_start: 0.9490 (mt) cc_final: 0.9022 (tt) REVERT: V 96 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7259 (tp) REVERT: W 32 LYS cc_start: 0.8757 (mttt) cc_final: 0.8107 (mtmm) REVERT: W 56 ASP cc_start: 0.8110 (p0) cc_final: 0.7740 (p0) REVERT: X 28 ARG cc_start: 0.8335 (ptm-80) cc_final: 0.7540 (ptm-80) outliers start: 160 outliers final: 131 residues processed: 808 average time/residue: 1.0586 time to fit residues: 1406.6289 Evaluate side-chains 856 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 715 time to evaluate : 4.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 2 residue 21 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 41 HIS Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 73 TYR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 32 ASN Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 553 optimal weight: 8.9990 chunk 582 optimal weight: 10.0000 chunk 531 optimal weight: 0.9990 chunk 566 optimal weight: 0.9980 chunk 341 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 445 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 512 optimal weight: 3.9990 chunk 536 optimal weight: 6.9990 chunk 564 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 GLN 6 20 ASN C 76 ASN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 HIS D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 GLN V 178 ASN W 29 GLN ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 102983 Z= 0.150 Angle : 0.549 10.259 155232 Z= 0.281 Chirality : 0.032 0.381 19969 Planarity : 0.005 0.080 7675 Dihedral : 23.410 179.778 54354 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.92 % Favored : 91.92 % Rotamer: Outliers : 4.24 % Allowed : 22.45 % Favored : 73.32 % 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: -1.99 (0.14), residues: 3156 helix: 0.32 (0.19), residues: 758 sheet: -1.28 (0.21), residues: 549 loop : -2.15 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 93 HIS 0.014 0.001 HIS D 130 PHE 0.014 0.001 PHE D 132 TYR 0.016 0.002 TYR 1 23 ARG 0.024 0.001 ARG G 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 739 time to evaluate : 4.071 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: 1 16 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7343 (mp0) REVERT: 1 29 ARG cc_start: 0.7158 (mmp80) cc_final: 0.6692 (mmp-170) REVERT: 1 53 GLU cc_start: 0.8235 (mp0) cc_final: 0.7967 (mp0) REVERT: 2 9 GLN cc_start: 0.8489 (tp40) cc_final: 0.7923 (mt0) REVERT: 3 58 VAL cc_start: 0.8777 (t) cc_final: 0.8556 (t) REVERT: C 62 TYR cc_start: 0.8459 (p90) cc_final: 0.7999 (p90) REVERT: C 95 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8285 (pp) REVERT: C 119 SER cc_start: 0.8254 (t) cc_final: 0.7930 (t) REVERT: C 192 THR cc_start: 0.8551 (m) cc_final: 0.8349 (p) REVERT: C 225 VAL cc_start: 0.8865 (m) cc_final: 0.8475 (t) REVERT: C 226 MET cc_start: 0.7963 (mtt) cc_final: 0.7714 (mtp) REVERT: E 192 TYR cc_start: 0.8476 (t80) cc_final: 0.8255 (t80) REVERT: E 196 ARG cc_start: 0.7718 (ttm170) cc_final: 0.7320 (ttm170) REVERT: F 84 PHE cc_start: 0.5401 (OUTLIER) cc_final: 0.4678 (p90) REVERT: F 159 MET cc_start: 0.4402 (pmm) cc_final: 0.4048 (pmm) REVERT: G 138 ASP cc_start: 0.5952 (t0) cc_final: 0.5486 (p0) REVERT: J 27 ARG cc_start: 0.6932 (mtm110) cc_final: 0.6497 (mtp180) REVERT: J 35 LEU cc_start: 0.8821 (mt) cc_final: 0.8601 (mp) REVERT: J 53 PHE cc_start: 0.8457 (m-80) cc_final: 0.8236 (m-80) REVERT: J 58 ASN cc_start: 0.7535 (t0) cc_final: 0.7000 (t0) REVERT: J 86 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8495 (ttpp) REVERT: J 89 ILE cc_start: 0.8051 (tt) cc_final: 0.7602 (tt) REVERT: J 119 GLN cc_start: 0.8294 (tt0) cc_final: 0.7950 (tm-30) REVERT: K 9 LYS cc_start: 0.8130 (mttt) cc_final: 0.7655 (mttt) REVERT: K 30 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8419 (ttt90) REVERT: K 65 THR cc_start: 0.9228 (m) cc_final: 0.8953 (p) REVERT: L 57 HIS cc_start: 0.8011 (m-70) cc_final: 0.7806 (m-70) REVERT: L 126 HIS cc_start: 0.6763 (m90) cc_final: 0.6109 (m90) REVERT: M 131 ILE cc_start: 0.8447 (mp) cc_final: 0.8059 (mp) REVERT: N 60 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8885 (tp) REVERT: N 117 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.5297 (mpt180) REVERT: O 23 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7871 (tptp) REVERT: O 55 VAL cc_start: 0.7272 (m) cc_final: 0.6986 (p) REVERT: P 88 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7306 (mmm160) REVERT: P 97 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7906 (m-10) REVERT: S 31 ILE cc_start: 0.8478 (mm) cc_final: 0.8271 (mm) REVERT: S 59 LYS cc_start: 0.8513 (mttt) cc_final: 0.8276 (mttt) REVERT: S 118 GLU cc_start: 0.5856 (tp30) cc_final: 0.4862 (tp30) REVERT: T 34 ARG cc_start: 0.7308 (ttp-170) cc_final: 0.7055 (ttm110) REVERT: T 73 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6399 (t80) REVERT: T 83 ILE cc_start: 0.9438 (mt) cc_final: 0.8990 (tt) REVERT: U 22 LYS cc_start: 0.8077 (tptp) cc_final: 0.7801 (tptp) REVERT: U 42 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7566 (mtmm) REVERT: V 96 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7254 (tp) REVERT: W 32 LYS cc_start: 0.8597 (mttt) cc_final: 0.8057 (mtmm) REVERT: X 28 ARG cc_start: 0.8283 (ptm-80) cc_final: 0.7695 (ptm-80) REVERT: Y 21 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8082 (mmm-85) REVERT: Y 31 ASN cc_start: 0.8583 (m-40) cc_final: 0.7923 (t0) REVERT: Y 53 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7524 (mm-30) REVERT: Z 30 ARG cc_start: 0.8053 (ptp-170) cc_final: 0.7782 (mtp85) outliers start: 110 outliers final: 85 residues processed: 789 average time/residue: 1.0095 time to fit residues: 1300.5223 Evaluate side-chains 808 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 715 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 21 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 73 TYR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 372 optimal weight: 4.9990 chunk 599 optimal weight: 0.8980 chunk 365 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 416 optimal weight: 20.0000 chunk 628 optimal weight: 5.9990 chunk 578 optimal weight: 9.9990 chunk 500 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 386 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 GLN 4 20 HIS C 76 ASN C 198 ASN D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 HIS ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 71 ASN ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 GLN ** U 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 102983 Z= 0.219 Angle : 0.581 12.192 155232 Z= 0.295 Chirality : 0.033 0.373 19969 Planarity : 0.005 0.090 7675 Dihedral : 23.410 178.783 54354 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.87 % Favored : 90.97 % Rotamer: Outliers : 4.24 % Allowed : 22.91 % Favored : 72.85 % 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: -1.99 (0.14), residues: 3156 helix: 0.27 (0.19), residues: 757 sheet: -1.21 (0.22), residues: 526 loop : -2.13 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 250 HIS 0.012 0.001 HIS D 130 PHE 0.026 0.002 PHE D 132 TYR 0.022 0.002 TYR O 102 ARG 0.013 0.001 ARG E 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 725 time to evaluate : 3.790 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: 1 16 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7595 (mp0) REVERT: 1 29 ARG cc_start: 0.7201 (mmp80) cc_final: 0.6659 (mtt90) REVERT: 1 53 GLU cc_start: 0.8227 (mp0) cc_final: 0.7946 (mp0) REVERT: 2 9 GLN cc_start: 0.8497 (tp40) cc_final: 0.7898 (mt0) REVERT: 3 3 LYS cc_start: 0.8046 (tttt) cc_final: 0.7665 (tttp) REVERT: C 62 TYR cc_start: 0.8527 (p90) cc_final: 0.8135 (p90) REVERT: C 95 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8334 (pp) REVERT: C 119 SER cc_start: 0.8383 (t) cc_final: 0.8048 (t) REVERT: C 192 THR cc_start: 0.8685 (m) cc_final: 0.8413 (p) REVERT: C 225 VAL cc_start: 0.8872 (m) cc_final: 0.8482 (t) REVERT: C 226 MET cc_start: 0.8047 (mtt) cc_final: 0.7830 (mtp) REVERT: E 192 TYR cc_start: 0.8578 (t80) cc_final: 0.8167 (t80) REVERT: E 196 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7202 (ttm170) REVERT: F 84 PHE cc_start: 0.5526 (OUTLIER) cc_final: 0.4760 (p90) REVERT: F 159 MET cc_start: 0.4546 (pmm) cc_final: 0.4154 (pmm) REVERT: G 138 ASP cc_start: 0.6052 (t0) cc_final: 0.5576 (p0) REVERT: G 140 GLN cc_start: 0.6817 (tp-100) cc_final: 0.6530 (tp-100) REVERT: J 27 ARG cc_start: 0.6964 (mtm110) cc_final: 0.6547 (mtp180) REVERT: J 53 PHE cc_start: 0.8460 (m-80) cc_final: 0.8232 (m-80) REVERT: J 58 ASN cc_start: 0.7463 (t0) cc_final: 0.6859 (t0) REVERT: J 86 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8430 (ttpp) REVERT: J 89 ILE cc_start: 0.8165 (tt) cc_final: 0.7708 (tt) REVERT: J 119 GLN cc_start: 0.8357 (tt0) cc_final: 0.7988 (tm-30) REVERT: K 9 LYS cc_start: 0.8176 (mttt) cc_final: 0.7702 (mttt) REVERT: K 30 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8429 (ttt90) REVERT: K 53 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7382 (mmtt) REVERT: K 65 THR cc_start: 0.9248 (m) cc_final: 0.8937 (p) REVERT: L 57 HIS cc_start: 0.7967 (m-70) cc_final: 0.7741 (m-70) REVERT: M 130 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7817 (mtp85) REVERT: M 134 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.4696 (mtp180) REVERT: N 60 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8926 (tp) REVERT: N 117 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.5381 (mpt180) REVERT: O 23 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7789 (tptp) REVERT: O 55 VAL cc_start: 0.7173 (m) cc_final: 0.6918 (p) REVERT: P 88 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7240 (mmm160) REVERT: P 97 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.7974 (m-10) REVERT: S 59 LYS cc_start: 0.8521 (mttt) cc_final: 0.8288 (mttt) REVERT: S 118 GLU cc_start: 0.5977 (tp30) cc_final: 0.4981 (tp30) REVERT: T 73 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6446 (t80) REVERT: T 83 ILE cc_start: 0.9455 (mt) cc_final: 0.8998 (tt) REVERT: V 96 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7273 (tp) REVERT: W 32 LYS cc_start: 0.8697 (mttt) cc_final: 0.8085 (mtmm) REVERT: X 28 ARG cc_start: 0.8235 (ptm-80) cc_final: 0.7493 (ptm-80) REVERT: Y 21 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8113 (mmm-85) REVERT: Y 31 ASN cc_start: 0.8500 (m-40) cc_final: 0.7962 (t0) REVERT: Y 53 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7572 (mm-30) outliers start: 110 outliers final: 94 residues processed: 774 average time/residue: 1.0050 time to fit residues: 1269.5963 Evaluate side-chains 816 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 713 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 0 residue 38 LYS Chi-restraints excluded: chain 2 residue 21 PHE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 43 ARG Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 36 ASP Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 73 TYR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 153 THR Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 33 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 36 ILE Chi-restraints excluded: chain Z residue 40 ASN Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 397 optimal weight: 0.9990 chunk 533 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 461 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 501 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 514 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN C 76 ASN D 183 HIS ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN M 123 HIS ** O 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119466 restraints weight = 173977.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122076 restraints weight = 74999.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122843 restraints weight = 45413.091| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 102983 Z= 0.421 Angle : 0.763 10.626 155232 Z= 0.378 Chirality : 0.040 0.457 19969 Planarity : 0.006 0.082 7675 Dihedral : 23.643 179.256 54354 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.22 % Favored : 88.59 % Rotamer: Outliers : 4.74 % Allowed : 22.99 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3156 helix: -0.15 (0.19), residues: 757 sheet: -1.44 (0.22), residues: 513 loop : -2.31 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP M 92 HIS 0.015 0.002 HIS D 130 PHE 0.037 0.003 PHE D 132 TYR 0.027 0.003 TYR O 102 ARG 0.017 0.001 ARG O 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19527.66 seconds wall clock time: 346 minutes 38.39 seconds (20798.39 seconds total)